Diagnosis of taeniasis is mainly using stool sample, particularly by identifying the eggs. However, this has limitation at the species level because tapeworms basically have similar eggs. Examination of the scolex or the gravid proglottids can resolve the exact species. But body segments are not often available, therefore, laborious histological observation of the uterine branches and PCR detection of ribosomal 5.8S gene are sometimes necessary. Ziehl–Neelsen stain is also used for "T. saginata" and "T. solium", in most cases only the former will stain, but the method is not entirely reliable. Loop-mediated isothermal amplification (LAMP) is highly sensitive (~2.5 times that of multiplex PCR), without false positives, for differentiating the taenid species from faecal samples.

To date the most relevant test for "T. asiatica" is by enzyme-linked immunoelectrotransfer blot (EITB). EITB can effectively identify asiatica from other taenid infections since the serological test indicates an immunoblot band of 21.5 kDa exhibited specifically by "T. asiatica". Even though it gives 100% sensitivity, it has not been tested with human sera for cross-reactivity, and it may show a high false positive result.

Sparganosis is typically diagnosed following surgical removal of the worms, although the infection may also be diagnosed by identification of eosinophilia or identification of the parasite in a tissue specimen. If such biopsy and excision procedures are not feasible, the antisparganum ELISA test may be used. In theory, a pre-operative diagnosis could be made by identification of exposure history and a painful, migratory, subcutaneous nodule. Sparganosis usually presents as a single nodule, while other cestode infections such as cysticercosis typically present as multiple nodules. Preoperative diagnosis, however, is rare.

CT and MRI scans are especially useful for diagnosis of cerebral sparganosis, as they reveal lesions in the brain. Through a retrospective analysis of 25 cases of cerebral sparganosis from 2000 to 2006, Song et al. found a number of characteristic signs that could be used in the future to diagnose cerebral sparganosis without performing an excision or tissue biopsy. The most characteristic finding was the "tunnel sign" on MRI images, showing the migrating track of the worm, while the most common finding was multiple conglomerated ring-shaped enhancements, seen as bead-shaped, usually with 3 to 6 rings. These findings led Song et al. to suggest that clinical history, ELISA, and either MRI or CT scans could be sufficient to make a sparganosis diagnosis. These lesions, however, are sometimes mistaken for tuberculosis lesions. In one case cerebral sparganosis was not diagnosed for four years, during which scans showed a cluster of rings moving from the right to the left side of the brain; ultimately the worm was found on biopsy.

Specific helminths can be identified through microscopic examination of their eggs (ova) found in faecal samples. The number of eggs is measured in units of eggs per gram. However, it does not quantify mixed infections, and in practice, is inaccurate for quantifying the eggs of schistosomes and soil-transmitted helmiths. Sophisticated tests such as serological assays, antigen tests, and molecular diagnosis are also available; however, they are time-consuming, expensive and not always reliable.

The traditional method of demonstrating either tapeworm eggs or proglottids in stool samples diagnoses only taeniasis, carriage of the tapeworm stage of the life cycle. Only a small minority of patients with cysticercosis will harbor a tapeworm, rendering stool studies ineffective for diagnosis. Ophthalmic cysticercosis can be diagnosed by visualizing parasite in eye by fundoscopy.

In cases of human cysticercosis, diagnosis is a sensitive problem and requires biopsy of the infected tissue or sophisticated instruments. "Taenia solium" eggs and proglottids found in feces, ELISA, or polyacrylamide gel electrophoresis diagnose only taeniasis and not cysticercosis. Radiological tests, such as X-ray, CT scans which demonstrate "ring-enhancing brain lesions", and MRIs, can also be used to detect diseases. X-rays are used to identify calcified larvae in the subcutaneous and muscle tissues, and CT scans and MRIs are used to find lesions in the brain.

Antibodies to cysticerci can be demonstrated in serum by EITB (Enzyme Linked Immunotransfer Blot) assay and in CSF by ELISA. An immunoblot assay using lentil-lectin (agglutinin from Lens culinaris) is highly sensitive and specific. However, Individuals with intracranial lesions and calcifications may be seronegative. In the CDC’s immunoblot assay, cysticercosis-specific antibodies can react with structural glycoprotein antigens from the larval cysts of "Taenia solium." However, this is mainly a research tool not widely available in clinical practice and nearly unobtainable in resource limited settings.

The fundamental prevention strategy is hygiene and sanitation. Secondary measures include stricter meat-inspection standards, livestock confinement, health education, safe meat preparation, mass drug therapy, and identifying and treating human and pig carriers. Moreover, a high level of sanitation and prevention of human faecal contamination of pig feeds also plays a major role in prevention. Infection can be prevented with proper disposal of human faeces around pigs, cooking meat thoroughly and/or freezing the meat at −10 °C for 5 days. For human cysticercosis, dirty hands are attributed to be the primary cause, and especially common among food handlers.

Proper cooking of meat is an effective prevention. For example, cooking (56 °C for 5 minutes) of beef viscera destroys cysticerci. Refrigeration, freezing (−10 °C for 9 days) or long periods of salting is also lethal to cysticerci. Inspection of beef and proper disposal of human excreta are also important measures.

Because this disease is so rare in humans, accurate diagnostic techniques have not been developed. CT scans and MRI’s are useful for detecting fluid filled cysts in all areas of the body, and some serological and microscopic tests can confirm the presence of "Taenia" larvae once surgery has taken place and a portion of the cyst can be removed to undergo examination and biopsy. Because of the lack of specificity in diagnostic technique, coenurosis can be misdiagnosed as neurocysticercosis or echinococcosis, other parasitic diseases affecting nervous system tissue.

An important consideration in diagnosing coenurosis properly is learning about the infected person’s exposure history. If the person presenting symptoms lives in an area with poor sanitation, high wild dog population, or known endemic tapeworm, his chance of having coenurosis is much higher. Also, this disease is seen more often in children than adults because children spend time outside in the mud and generally are more likely than adults to come into contact with canid feces.

Microscopic identification of eggs in the stool is the basis of specific diagnosis. Eggs are usually numerous and can be demonstrated without concentration techniques. Examination of proglottids passed in the stool is also of diagnostic value.

Diagnostic tool:

- Microscopy

- Morphologic comparison with other intestinal parasites

Though it is difficult to identify the eggs or proglottids to the species level, the distinction is of little medical importance because, like most adult tapeworms in the intestine, all members of this genus respond to the same drugs.

Avoid ingestion of raw freshwater fish. Adequate cooking or freezing of freshwater fish will kill the encysted fish tapeworm larvae. Also, because human feces is an important mechanism for spreading eggs, proper disposal of sewage can cut down on infection of fish and thus of humans.

One treatment for sparganosis is praziquantel, administered at a dose of 120 to 150 mg/kg body weight over 2 days; however, praziquantel has had limited success. In general, infestation by one or a few sparganum larvae is often best treated by surgical removal.

DNA analysis of rare worms removed surgically can provide genome information to identify and characterise each parasite; treatments for the more common tapeworms can be cross-checked to see whether they are also likely to be effective against the species in question.

The disease is more complicated and severe when the oncospheres settle in the CNS tissue. This makes operating more difficult than when the disease presents in the muscles or subcutaneous tissues. The most common and widely recognized treatment for this disease is surgical removal of the cysts. However, this is not always possible. Other treatments that have seen positive results are Praziquantel and Albendazole. Praziquantel causes cell membranes of worms to become permeable. In this way the worm loses intracellular calcium. This in turn causes the worm to become paralyzed. Albendazole causes the worm to produce less ATP eventually leading to its death. Glucocorticoids can be used to help subdue the inflammatory symptoms of the disease.

In regions where helminthiasis is common, mass deworming treatments may be performed, particularly among school-age children, who are a high-risk group. Most of these initiatives are undertaken by the World Health Organization (WHO) with positive outcomes in many regions. Deworming programs can improve school attendance by 25 percent. Although deworming improves the health of an individual, outcomes from mass deworming campaigns, such as reduced deaths or increases in cognitive ability, nutritional benefits, physical growth, and performance, are uncertain or not apparent.

Tapeworms are treated with medications taken by mouth, usually in a single dose. The drug of choice for tapeworm infections is praziquantel. Niclosamide can also be used.

A formal diagnose of any type of echinococcosis requires a combination of tools that involve imaging techniques, histopathology, or nucleic acid detection and serology. For cystic echinococcosis diagnosis, imaging is the main method—while serology tests (such as indirect hemogglutination, ELISA (enzyme linked immunosorbent assay), immunoblots or latex agglutination) that use antigens specific for "E. granulosus" verify the imaging results. The imaging technique of choice for cystic echinococcosis is ultrasonography, since it is not only able to visualize the cysts in the body's organs, but it is also inexpensive, non-invasive and gives instant results. In addition to ultrasonography, both MRI and CT scans can and are often used although an MRI is often preferred to CT scans when diagnosing cystic echinococcosis since it gives better visualization of liquid areas within the tissue.

As with cystic echinococcosis, ultrasonography is the imaging technique of choice for alveolar echinococcosis and is usually complemented by CT scans since CT scans are able to detect the largest number of lesions and calcifications that are characteristic of alveolar echinococcosis. MRIs are also used in combination with ultrasonography though CT scans are preferred. Like cystic echinococcosis, imaging is the major method used for the diagnosis of alveolar echinococcosis while the same types of serologic tests (except now specific for "E. multilocularis" antigens) are used to verify the imaging results. It is also important to note that serologic tests are more valuable for the diagnosis of alveolar echinococcosis than for cystic echinococcosis since they tend to be more reliable for alveolar echinococcosis since more antigens specific for "E. multilocularis" are available. In addition to imaging and serology, identification of "E. multilocularis" infection via PCR or a histological examination of a tissue biopsy from the patient is another way to diagnose alveolar echinococcosis.

Cure rates are extremely good with modern treatments, but successful cure results may be of no symptomatic benefit to patients.

The two drugs that have been well-described for the treatment of hymenolepiasis are praziquantel and niclosamide. Praziquantel, which is parasiticidal in a single dose for all the stages of the parasite, is the drug of choice because it acts very rapidly against "H. nana". Although structurally unrelated to other anthelminthics, it kills both adult worms and larvae. "In vitro", the drug produces vacuolization and disruption of the tegument in the neck of the worms, but not in more posterior portions of the strobila. Praziquantel is well absorbed when taken orally, and it undergoes first-pass metabolism and 80% of the dose is excreted as metabolites in urine within 24 hours.

Repeated treatment is required for "H. nana" at an interval of 7–10 days.

Praziquantel as a single dose (25 mg/kg) is the current treatment of choice for hymenolepiasis and has an efficacy of 96%. Single-dose albendazole (400 mg) is also very efficacious (>95%).

A three-day course of nitazoxanide is 75–93% efficacious. The dose is 1 g daily for adults and children over 12; 400 mg daily for children aged 4 to 11 years; and 200 mg daily for children aged 3 years or younger.

Most occurrences are found in areas that lack adequate sanitation and include Southeast Asia, West Africa, and East Africa.

The following diagnostic methods are not routinely available to patients. Researchers have reported that they are more reliable at detecting infection, and in some cases can provide the physician with information to help determine whether "Blastocystis" infection is the cause of the patient's symptoms:

Serum antibody testing: A 1993 research study performed by the NIH with United States patients suggested that it was possible to distinguish symptomatic and asymptomatic infection with "Blastocystis" using serum antibody testing. The study used blood samples to measure the patient's immune reaction to chemicals present on the surface of the "Blastocystis" cell. It found that patients diagnosed with symptomatic "Blastocystis" infection exhibited a much higher immune response than controls who had "Blastocystis" infection but no symptoms. The study was repeated in 2003 at Ain Shams University in Egypt with Egyptian patients with equivalent results.

Fecal antibody testing: A 2003 study at Ain Shams University in Egypt indicated that patients symptomatically infected could be distinguished with a fecal antibody test. The study compared patients diagnosed with symptomatic "Blastocystis" infection to controls who had "Blastocystis" infection but no symptoms. In the group with symptoms, IgA antibodies to "Blastocystis" were detected in fecal specimens that were not present in the healthy control group.

Stool culture: Culturing has been shown to be a more reliable method of identifying infection. In 2006, researchers reported the ability to distinguish between disease causing and non-disease causing isolates of "Blastocystis" using stool culture. "Blastocystis" cultured from patients who were sick and diagnosed with "Blastocystis" infection produced large, highly adhesive amoeboid forms in culture. These cells were absent in "Blastocystis" cultures from healthy controls. Subsequent genetic analysis showed the "Blastocystis" from healthy controls was genetically distinct from that found in patients with symptoms. Protozoal culture is unavailable in most countries due to the cost and lack of trained staff able to perform protozoal culture.

Genetic analysis of isolates: Researchers have used techniques which allow the DNA of "Blastocystis" to be isolated from fecal specimens. This method has been reported to be more reliable at detecting "Blastocystis" in symptomatic patients than stool culture. This method also allows the species group of "Blastocystis" to be identified. Research is continuing into which species groups are associated with symptomatic (see Genetics and Symptoms) blastocystosis.

Immuno-fluorescence (IFA) stain: An IFA stain causes "Blastocystis" cells to glow when viewed under a microscope, making the diagnostic method more reliable. IFA stains are in use for Giardia and Cryptosporidium for both diagnostic purposes and water quality testing. A 1991 paper from the NIH described the laboratory development of one such stain. However, no company currently offers this stain commercially.

Anecdotal data gathered from helminth self-treaters and their physicians and presented in socio-medical studies suggest that a much larger number of diseases may be amenable to helminthic therapy than are currently being investigated by formal clinical trials.

Diagnosis is performed by determining if the infection is present, and then making a decision as to whether the infection is responsible for the symptoms. Diagnostic methods in clinical use have been reported to be of poor quality and more reliable methods have been reported in research papers.

For identification of infection, the only method clinically available in most areas is the "Ova and Parasite" (O&P) exam, which identifies the presence of the organism by microscopic examination of a chemically preserved stool specimen. This method is sometimes called "Direct Microscopy". In the United States, pathologists are required to report the presence of "Blastocystis" when found during an O&P exam, so a special test does not have to be ordered. Direct Microscopy is inexpensive, as the same test can identify a variety of gastrointestinal infections, such as "Giardia", "Entamoeba histolytica", "Cryptosporidium". However one laboratory director noted that pathologists using conventional microscopes failed to identify many "Blastocystis" infections, and indicated the necessity for special microscopic equipment for identification. The following table shows the sensitivity of Direct Microscopy in detecting "Blastocystis" when compared to stool culture, a more sensitive technique. Stool culture was considered by some researchers to be the most reliable technique, but a recent study found stool culture only detected 83% of individuals infected when compared to polymerase chain reaction (PCR) testing.

Reasons given for the failure of Direct Microscopy include: (1) Variable Shedding: The quantity of "Blastocystis" organisms varies substantially from day to day in infected humans and animals; (2) Appearance: Some forms of "Blastocystis" resemble fat cells or white blood cells, making it difficult to distinguish the organism from other cells in the stool sample; (3) Large number of morphological forms: "Blastocystis" cells can assume a variety of shapes, some have been described in detail only recently, so it is possible that additional forms exist but have not been identified.

Several methods have been cited in literature for determination of the significance of the finding of "Blastocystis":

1. Diagnosis only when large numbers of organism present: Some physicians consider "Blastocystis" infection to be a cause of illness only when large numbers are found in stool samples. Researchers have questioned this approach, noting that it is not used with any other protozoal infections, such as "Giardia" or "Entamoeba histolytica". Some researchers have reported no correlation between number of organisms present in stool samples and the level of symptoms. A study using polymerase chain reaction testing of stool samples suggested that symptomatic infection can exist even when sufficient quantities of the organism do not exist for identification through Direct Microscopy.

2. Diagnosis-by-exclusion: Some physicians diagnose "Blastocystis" infection by excluding all other causes, such as infection with other organisms, food intolerances, colon cancer, etc. This method can be time consuming and expensive, requiring many tests such as endoscopy and colonoscopy.

3. Disregarding "Blastocystis" : In the early to mid-1990s, some US physicians suggested all findings of "Blastocystis" are insignificant. No recent publications expressing this opinion could be found.

Diagnosis of toxoplasmosis in humans is made by biological, serological, histological, or molecular methods, or by some combination of the above. Toxoplasmosis can be difficult to distinguish from primary central nervous system lymphoma. It mimics several other infectious diseases so clinical signs are non-specific and are not sufficiently characteristic for a definite diagnosis. As a result, the diagnosis is made by a trial of therapy (pyrimethamine, sulfadiazine, and folinic acid (USAN: leucovorin)), if the drugs produce no effect clinically and no improvement on repeat imaging.

"T. gondii" may also be detected in blood, amniotic fluid, or cerebrospinal fluid by using polymerase chain reaction. "T. gondii" may exist in a host as an inactive cyst that would likely evade detection.

Serological testing can detect "T. gondii" antibodies in blood serum, using methods including the Sabin–Feldman dye test (DT), the indirect hemagglutination assay, the indirect fluorescent antibody assay (IFA), the direct agglutination test, the latex agglutination test (LAT), the enzyme-linked immunosorbent assay (ELISA), and the immunosorbent agglutination assay test (IAAT).

The most commonly used tests to measure IgG antibody are the DT, the ELISA, the IFA, and the modified direct agglutination test. IgG antibodies usually appear within a week or two of infection, peak within one to two months, then decline at various rates. "Toxoplasma" IgG antibodies generally persist for life, and therefore may be present in the bloodstream as a result of either current or previous infection.

To some extent, acute toxoplasmosis infections can be differentiated from chronic infections using an IgG avidity test, which is a variation on the ELISA. In the first response to infection, toxoplasma-specific IgG has a low affinity for the toxoplasma antigen; in the following weeks and month, IgG affinity for the antigen increases. Based on the IgG avidity test, if the IgG in the infected individual has a high affinity, it means that the infection began three to five months before testing. This is particularly useful in congenital infection, where pregnancy status and gestational age at time of infection determines treatment.

In contrast to IgG, IgM antibodies can be used to detect acute infection, but generally not chronic infection. The IgM antibodies appear sooner after infection than the IgG antibodies and disappear faster than IgG antibodies after recovery. In most cases, "T. gondii"-specific IgM antibodies can first be detected approximately a week after acquiring primary infection, and decrease within one to six months; 25% of those infected are negative for "T. gondii"-specific IgM within seven months. However, IgM may be detectable months or years after infection, during the chronic phase, and false positives for acute infection are possible. The most commonly used tests for the measurement of IgM antibody are double-sandwich IgM-ELISA, the IFA test, and the immunosorbent agglutination assay (IgM-ISAGA). Commercial test kits often have low specificity, and the reported results are frequently misinterpreted.

The capture, transportation and culture of bait fish can spread damaging organisms between ecosystems, endangering them. In 2007, several American states, including Michigan, enacted regulations designed to slow the spread of fish diseases, including viral hemorrhagic septicemia, by bait fish. Because of the risk of transmitting "Myxobolus cerebralis" (whirling disease), trout and salmon should not be used as bait. Anglers may increase the possibility of contamination by emptying bait buckets into fishing venues and collecting or using bait improperly. The transportation of fish from one location to another can break the law and cause the introduction of fish and parasites alien to the ecosystem.

Evidence in support of the idea that helminthic infections reduce the severity of autoimmune diseases is primarily derived from animal models. Studies conducted on mice and rat models of colitis, muscular sclerosis, type 1 diabetes, and asthma have shown helminth-infected subjects to display protection from the disease. While helminths are often considered a homogenous group, considerable differences exist between species and the utilization of species in clinical research varies between human and animal trials. As such, caution must be exercised when interpreting the results from animal models.

Helminthic therapy is currently being studied as a treatment for several (non-viral) autoimmune diseases in humans including celiac disease, Crohn's disease, multiple sclerosis, ulcerative colitis, and atherosclerosis. It is currently unknown which clinical dose or species of helminth is the most effective method of treatment. Hookworms have been linked to reduced risk of developing asthma, while "Ascaris lumbricoides" (roundworm infection) was associated with an "increased" risk of asthma. Similarly, "Hymenolepis nana", "Trichoris trichiura", "Ascaris lumbricoides", "Strongyloides stercolaris", "Enterobius vermicularis", and "Trichuris suis" ova have all been found to lower the number of symptom exacerbations, reduce the number of symptom relapses, and decrease the number of new or enlarging brain lesions in patients with multiple sclerosis at doses ranging from 1,180 to 9,340 eggs per gram. However, "Ascaris lumbricoides", "Strongyloides stercolaris" and "Enterobius vermicularis" are not considered suitable for therapeutic use in humans because they do not meet the criteria for a therapeutic helminth.

"Trichuris suis" ova has been used in most cases to treat autoimmune disorders because it is thought to be non-pathogenic in humans and therefore has been rendered as safe.

The use of "Trichuris suis" ova has been granted by the USA Food and Drug Administration as an investigational medicinal product (IMP). While in the UK, the hookworm "Necator americanus" has been granted an IMP license by the Medicines and Healthcare Regulatory Authority. This hookworm is likely to be relatively safe, although it can cause temporary gastrointestinal side effects, especially following the initial inoculation and with larger doses.

The general ideal characteristics for a therapeutic helminth are as follows:

- Little or no pathogenic potential

- Does not multiply in the host

- Cannot be directly spread to close contacts

- Produces a self-limited colonization in humans

- Produces an asymptomatic colonization in humans

- Does not alter behaviour in patients with depressed immunity

- Is not affected by most commonly used medications

- Can be eradicated with an anti-helminthic drug

- Can be isolated free of other potential pathogens

- Can be isolated or produced in large numbers

- Can be made stable for transport and storage

- Easy to administer

Biotechnology companies in the developing world have targeted neglected tropical diseases due to need to improve global health.

Mass drug administration is considered a possible method for eradication, especially for lymphatic filariasis, onchocerciasis, and trachoma, although drug resistance is a potential problem. According to Fenwick, Pfizer donated 70 million doses of drugs in 2011 to eliminate trachoma through the International Trachoma Initiative. Merck has helped The African Programme for the Control of Onchocerciasis (APOC) and Oncho Elimination Programme for the Americas to greatly diminished the effect of Onchocerciasis by donating ivermectin. Merck KGaA pledged to give 200 million tablets of praziquantel over 10 years, the only cure for schistosomiasis. GlaxoSmithKline has donated two billion tablets of medicine for lymphatic filariasis and pledged 400 million deworming tablets per year for five years in 2010. Johnson & Johnson has pledged 200 million deworming tablets per year. Novartis has pledged leprosy treatment, EISAI pledged two billion tablets to help treat lymphatic filariasis.