For botulism in babies, diagnosis should be made on signs and symptoms. Confirmation of the diagnosis is made by testing of a stool or enema specimen with the mouse bioassay.

Physicians may consider diagnosing botulism if the patient's history and physical examination suggest botulism. However, these clues are often not enough to allow a diagnosis. Other diseases such as Guillain–Barré syndrome, stroke, and myasthenia gravis can appear similar to botulism, and special tests may be needed to exclude these other conditions. These tests may include a brain scan, cerebrospinal fluid examination, nerve conduction test (electromyography, or EMG), and an edrophonium chloride (Tensilon) test for myasthenia gravis. A definite diagnosis can be made if botulinum toxin is identified in the food, stomach or intestinal contents, vomit or feces. The toxin is occasionally found in the blood in peracute cases. Botulinum toxin can be detected by a variety of techniques, including enzyme-linked immunosorbent assays (ELISAs), electrochemiluminescent (ECL) tests and mouse inoculation or feeding trials. The toxins can be typed with neutralization tests in mice. In toxicoinfectious botulism, the organism can be cultured from tissues. On egg yolk medium, toxin-producing colonies usually display surface iridescence that extends beyond the colony.

In adults, botulism can be treated by passive immunization with a horse-derived antitoxin, which blocks the action of the toxin circulating in the blood. A trivalent antitoxin containing antibodies raised against botulinum toxin types A, B, and E is used most commonly, however a heptavalent botulism antitoxin has also been developed and was approved by the U.S. FDA in 2013. In infants, horse-derived antitoxin is sometimes avoided for fear of infants developing serum sickness or lasting hypersensitivity to horse-derived proteins. To avoid this, a human-derived antitoxin has been developed and approved by the U.S. FDA in 2003 for the treatment of infant botulism. This human-derived antitoxin has been shown to be both safe and effective for the treatment of infant botulism. However, the danger of equine-derived antitoxin to infants has not been clearly established, and one study showed the equine-derived antitoxin to be both safe and effective for the treatment of infant botulism.

Trivalent (A,B,E) botulinum antitoxin is derived from equine sources utilizing whole antibodies (Fab and Fc portions). In the United States, this antitoxin is available from the local health department via the CDC. The second antitoxin, heptavalent (A,B,C,D,E,F,G) botulinum antitoxin, is derived from "despeciated" equine IgG antibodies which have had the Fc portion cleaved off leaving the F(ab')2 portions. This less immunogenic antitoxin is effective against all known strains of botulism where not contraindicated.

The presence of avian botulism is extremely hard to detect before an outbreak. Frequent surveillance of sites at risk is needed for early detection of the disease in order to take action and remove carcasses. Vaccines are also developed, but they are expected to have limited effectiveness in stemming outbreaks in wild waterbird populations. However may be effective in reducing mortality for endangered island waterfowl and small non-migratory wild populations. Field tests are needed.

The botulinum neurotoxin is lethal because it causes paralysis. Field identification involves locating birds showing flaccidity in the legs, wings and neck, as well as the presence of protuberant nictitating membrane. The presence of several dozen, or even hundreds, of fresh waterbird carcasses is the stereotypical sign an outbreak has occurred. In this case the specimens need to be taken to disease laboratory to determine the cause of mortality. Most commonly, detection of "C. botulinum" in carcasses during lab work is accomplished through analysis of polymerase chain reactions (PCR) and is often the most successful method.

An epidemiological investigation can be done to determine a patient's exposure to raw infected meat. Often, an infection arises from home-preparation of contaminated meat, in which case microscopy of the meat may be used to determine the infection. Exposure determination does not have to be directly from a laboratory-confirmed infected animal. Indirect exposure criteria include the consumption of products from a laboratory-confirmed infected animal, or sharing of a common exposure with a laboratory-confirmed infected human.

Diagnosis of trichinosis is confirmed by a combination of exposure history, clinical diagnosis, and laboratory testing.

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.

Enteroinvasive "Escherichia coli" (EIEC) is a type of pathogenic bacteria whose infection causes a syndrome that is identical to shigellosis, with profuse diarrhea and high fever. EIEC are highly invasive, and they use adhesin proteins to bind to and enter intestinal cells. They produce no toxins, but severely damage the intestinal wall through mechanical cell destruction.

It is closely related to "Shigella".

After the "E. coli" strain penetrates through the epithelial wall, the endocytosis vacuole gets lysed, the strain multiplies using the host cell machinery, and extends to the adjacent epithelial cell. In addition, the plasmid of the strain carries genes for a type III secretion system that is used as the virulent factor. Although it is an invasive disease, the invasion usually does not pass the submucosal layer. The similar pathology to shigellosis may be because both strains of bacteria share some virulent factors. The invasion of the cells can trigger a mild form of diarrhea or dysentery, often mistaken for dysentery caused by "Shigella" species. The illness is characterized by the appearance of blood and mucus in the stools of infected individuals or a condition called colitis.

Dysentery caused by EIEC usually occurs within 12 to 72 hours following the ingestion of contaminated food. The illness is characterized by abdominal cramps, diarrhea, vomiting, fever, chills, and a generalized malaise. Dysentery caused by this organism is generally self-limiting with no known complications.

Enterovirulent classes of "E. coli" are referred to as the EEC group (enterovirulent "E. coli"):

1. Enteroinvasive "E. coli" (EIEC) invades (passes into) the intestinal wall to produce severe diarrhea.

2. Enterohemorrhagic "E. coli" (EHEC): A type of EHEC, "E. coli" 0157:H7, can cause bloody diarrhea and hemolytic uremic syndrome (anemia and kidney failure).

3. Enterotoxigenic "E. coli" (ETEC) produces a toxin that acts on the intestinal lining, and is the most common cause of traveler's diarrhea.

4. Enteropathogenic "E. coli" (EPEC) can cause diarrhea outbreaks in newborn nurseries.

5. Enteroaggregative "E. coli" (EAggEC) can cause acute and chronic (long-lasting) diarrhea in children.

It is currently unknown what foods may harbor EIEC, but any food contaminated with human feces from an ill individual, either directly or via contaminated water, could cause disease in others. Outbreaks have been associated with hamburger meat and unpasteurized milk.

Under most situations, infection is hard to recognize because the symptoms are mild or even absent. In humans and wild animals, infection is not easily identified. Especially the adult flukes, even if in large number, generally do not cause complications. There is not yet a standard diagnostic test. Therefore, manual diagnosis is done at many levels. Diagnosis basically relies on a combination of postmortem analyses, clinical signs displayed by the animals, and response to drenching. In heavy infection, symptoms are easily observed in sheep and cattle as they become severely anorexic or inefficiently digest food, and become unthrifty. Copious fetid diarrhea is an obvious indication, as the soiling of hind legs and tails with fluid feces are readily noticeable. Even though it not always the case, immature flukes can be identified from the fluid excrement. On rare occasions, eggs can be identified from stools of suspected animals. In developing countries diagnosis and prognosis is often hindered by multiple infections with other trematodes, such as "Fasciola hepatica" and schistosomes, because these flukes are given primary importance due to their pervasive nature.

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.

Metagonimiasis is diagnosed by eggs seen in feces. Only after antihelminthic treatment will adult worms be seen in the feces, and then can be used as part of a diagnostic procedure. A 1993 analysis of the efficacy of ELISA tests to diagnose metagonimiasis implied that simultaneous screening of specific antibodies to several parasite agents are important in serological diagnosis of acute parasitic disease and more research should be done on the efficacy of these methods of diagnosis.

Diagnosis may be difficult because the egg-laying capacity of heterophyids is limited, and therefore sedimentation concentration procedures may be needed to demonstrate eggs in lighter infections. Accurate species identification is also difficult because eggs of most flukes are similar in size and morphology, especially those of "Heterophyes heterophyes", "Clonorchis" and "Opisthorchis". It is important to ask where the person may have contracted the disease, find out if they have been to en endemic area, and check for signs and symptoms that would lead to metagonimiasis.

Most immunodiagnostic tests will detect infection and have a sensitivity above 90% during all stages of the diseases. In addition antibody concentration quickly drops post treatment and no antibodies are present one year after treatment, which makes it a very good diagnostic method. In humans, diagnosis of fasciolosis is usually achieved parasitologically by findings the fluke eggs in stool, and immunologically by ELISA and Western blot. Coprological examinations of stool alone are generally not adequate because infected humans have important clinical presentations long before eggs are found in the stools.

Moreover, in many human infections, the fluke eggs are often not found in the faeces, even after multiple faecal examinations. Furthermore, eggs of "F. hepatica", "F. gigantica" and "Fasciolopsis buski" are morphologically indistinguishable. Therefore, immunonological methods such ELISA and enzyme-linked immunoelectrotransfer blot, also called Western blot, are the most important methods in diagnosis of "F. hepatica" infection. These immunological tests are based on detection of species-specific antibodies from sera. The antigenic preparations used have been primarily derived from extracts of excretory/secretory products from adult worms, or with partially purified fractions. Recently, purified native and recombinant antigens have been used, e.g. recombinant "F. hepatica" cathepsin L-like protease.

Methods based on antigen detection (circulating in serum or in faeces) are less frequent. In addition, biochemical and haematological examinations of human sera support the exact diagnosis (eosinophilia, elevation of liver enzymes). Ultrasonography and xray of the abdominal cavity, biopsy of liver, and gallbladder punctuate can also be used (ref: US-guided gallbladder aspiration:

a new diagnostic method for biliary fascioliasis. A. Kabaalioglu, A. Apaydin, T. Sindel, E. Lüleci. Eur. Radiol. 9, 880±882 (1999) . False fasciolosis (pseudofasciolosis) refers to the presence of eggs in the stool resulting not from an actual infection but from recent ingestion of infected livers containing eggs. This situation (with its potential for misdiagnosis) can be avoided by having the patient follow a liver-free diet several days before a repeat stool examination.

In animals, intravital diagnosis is based predominantly on faeces examinations and immunological methods. However, clinical signs, biochemical and haematological profile, season, climate conditions, epidemiology situation, and examinations of snails must be considered. Similarly to humans, faeces examinations are not reliable. Moreover, the fluke eggs are detectable in faeces 8–12 weeks post-infection. In spite of that fact, faecal examination is still the only used diagnostic tool in some countries. While coprological diagnosis of fasciolosis is possible from 8- to 12-week post-infection (WPI), "F. hepatica" specific-antibodies are recognized using ELISA or Western blot after 2-4 week post-infection. Therefore, these methods provide early detection of the infection.

For medical purposes, the exact number of helminth eggs is less important and therefore most diagnoses are made simply by identifying the appearance of the worm or eggs in feces. Due to the large quantity of eggs laid, physicians can diagnose using only one or two fecal smears. The Kato technique (also called the Kato-Katz technique) is a laboratory method for preparing human stool samples prior to searching for parasite eggs. Eggs per gram is a laboratory test that determines the number of eggs per gram of feces in patients suspected of having a parasitological infection, such as schistosomiasis.

For the purpose of setting treatment standards and reuse legislation, it is important to be able to determine the amount of helminth eggs in an environmental sample with some accuracy. The detection of viable helminth eggs in samples of wastewater, sludge or fresh feces (as a diagnostic tool for the infection helminthiasis) is not straight forward. In fact, many laboratories in developing countries lack the right equipment or skilled staff required to do so. An important step in the analytical methods is usually the concentration of the eggs in the sample, especially in the case of wastewater samples. A concentration step may not be required in samples of dried feces, e.g. samples collected from urine-diverting dry toilets.

Antibody detection can be useful to indicate schistosome infection in people who have traveled to areas where schistosomiasis is common and in whom eggs cannot be demonstrated in fecal or urine specimens. Test sensitivity and specificity vary widely among the many tests reported for the serologic diagnosis of schistosomiasis and are dependent on both the type of antigen preparations used (crude, purified, adult worm, egg, cercarial) and the test procedure.

At CDC, a combination of tests with purified adult worm antigens is used for antibody detection. All serum specimens are tested by FAST-ELISA using "S. mansoni" adult microsomal antigen (MAMA). A positive reaction (greater than 9 units/µl serum) indicates infection with "Schistosoma" species. Sensitivity for "S. mansoni" infection is 99 percent, 95 percent for "S. haematobium" infection, and less than 50 percent for "S. japonicum" infection. Specificity of this assay for detecting schistosome infection is 99 percent. Because test sensitivity with the FAST-ELISA is reduced for species other than "S. mansoni", immunoblots of the species appropriate to the patient's travel history are also tested to ensure detection of "S. haematobium" and "S. japonicum" infections. Immunoblots with adult worm microsomal antigens are species-specific and so a positive reaction indicates the infecting species. The presence of antibody is indicative only of schistosome infection at some time and cannot be correlated with clinical status, worm burden, egg production, or prognosis. Where a person has traveled can help determine what "Schistosoma" species to test for by immunoblot.

In 2005, a field evaluation of a novel handheld microscope was undertaken in Uganda for the diagnosis of intestinal schistosomiasis by a team led by Russell Stothard from the Natural History Museum of London, working with the Schistosomiasis Control Initiative, London.

"Ascaris" takes most of its nutrients from the partially digested host food in the intestine. There is some evidence that it can secrete anti-enzymes, presumably to protect itself from digestion by the hosts' enzymes. Children are often more severely affected.

Diagnosis rests on the microscopic identification of larvae (rhabditiform and occasionally filariform) in the stool or duodenal fluid. Examination of many samples may be necessary, and not always sufficient, because direct stool examination is relatively insensitive, with a single sample only able to detect larvae in about 25% of cases. It can take 4 weeks from initial infection to the passage of larvae in the stool.

The stool can be examined in wet mounts:

- directly

- after concentration (formalin-ethyl acetate)

- after recovery of the larvae by the Baermann funnel technique

- after culture by the Harada-Mori filter paper technique

- after culture in agar plates

Culture techniques are the most sensitive, but are not routinely available in the West. In the UK, culture is available at either of the Schools of Tropical Medicine in Liverpool or London. Direct examination must be done on stool that is freshly collected and not allowed to cool down, because hookworm eggs hatch on cooling and the larvae are very difficult to distinguish from Strongyloides.

Finding Strongyloides in the stool is negative in up to 70% of tests. It is important to undergo frequent stool sampling as well as duodenal biopsy if a bad infection is suspected. The duodenal fluid can be examined using techniques such as the Enterotest string or duodenal aspiration. Larvae may be detected in sputum from patients with disseminated strongyloidiasis.

Given the poor ability of stool examination to diagnose strongyloides, detecting antibodies by ELISA can be useful. Serology can cross-react with other parasites, remain positive for years after successful treatment or be falsely negative in immunocompromised patients. Infected patients will also often have an elevated eosinophil count, with an average of absolute eosinophil count of 1000 in one series. The combination of clinical suspicion, a positive antibody and a peripheral eosinophilia can be strongly suggestive of infection.

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.

Gastroscopy, or endoscopic evaluation of the stomach, is useful in chronic cases of colic suspected to be caused by gastric ulcers, gastric impactions, and gastric masses. A 3-meter scope is required to visualize the stomach of most horses, and the horse must be fasted prior to scoping.

Diagnosis depends on finding the eggs or the adult pinworms. Individual eggs are invisible to the naked eye, but they can be seen using a low-power microscope. On the other hand, the light-yellowish thread-like adult pinworms are clearly visually detectable, usually during the night when they move near the anus, or on toilet paper. Transparent adhesive tape (e.g. Scotch Tape) applied on the anal area will pick up deposited eggs, and diagnosis can be made by examining the tape with a microscope. This test is most successful if done every morning for several days, because the females do not lay eggs every day, and the number of eggs vary.

Pinworms do not lay eggs in the feces, but sometimes eggs are deposited in the intestine. As such, routine examination of fecal material gives a positive diagnosis in only 5 to 15% of infected subjects, and is therefore of little practical diagnostic use. In a heavy infection, female pinworms may adhere to stools that pass out through the anus, and they may thus be detected on the surface on the stool. Adult pinworms are occasionally seen during colonoscopy. On a microscopic level, pinworms have an identifying feature of alae (i.e., protruding ridges) running the length of the worm.

Most diagnoses are made by identifying the appearance of the worm or eggs in feces. Due to the large quantity of eggs laid, physicians can diagnose using only one or two fecal smears.

The diagnosis is usually incidental when the host passes a worm in the stool or vomit. The eggs can be seen in a smear of fresh feces examined on a glass slide under a microscope and there are various techniques to concentrate them first or increase their visibility, such as the ether sedimentation method or the Kato technique. The eggs have a characteristic shape: they are oval with a thick, mamillated shell (covered with rounded mounds or lumps), measuring 35-50 micrometer in diameter and 40-70 in length. During pulmonary disease, larvae may be found in fluids aspirated from the lungs. White blood cells counts may demonstrate peripheral eosinophilia; this is common in many parasitic infections and is not specific to ascariasis. On X-ray, 15–35 cm long filling defects, sometimes with whirled appearance (bolus of worms).

Due to the wide variety of intestinal parasites, a description of the symptoms rarely is sufficient for diagnosis. Instead, medical personnel use one of two common tests: they search stool samples for the parasites, or apply an adhesive the anus to search for eggs.

Radiographs (x-rays) are sometimes used to look for sand and enteroliths. Due to the size of the adult horse's abdomen, it requires a powerful machine that is not available to all practitioners. Additionally, the quality of these images is sometimes poor.

Major groups of parasites include protozoans (organisms having only one cell) and parasitic worms (helminths). Of these, protozoans, including cryptosporidium, microsporidia, and isospora, are most common in HIV-infected persons. Each of these parasites can infect the digestive tract, and sometimes two or more can cause infection at the same time.

Diagnosis of infection is confirmed by the identification of eggs in stools. Eggs of "S. mansoni" are approximately 140 by 60 µm in size, and have a lateral spine. The diagnosis is improved by the use of the Kato-Katz technique (a semi-quantitative stool examination technique). Other methods that can be used are enzyme-linked immunosorbent assay (ELISA), circumoval precipitation test, and alkaline phosphatase immunoassay.

Microscopic identification of eggs in stool or urine is the most practical method for diagnosis. Stool examination should be performed when infection with "S. mansoni" or "S. japonicum" is suspected, and urine examination should be performed if "S. haematobium" is suspected. Eggs can be present in the stool in infections with all "Schistosoma" species. The examination can be performed on a simple smear (1 to 2 mg of fecal material). Since eggs may be passed intermittently or in small amounts, their detection will be enhanced by repeated examinations and/or concentration procedures. In addition, for field surveys and investigational purposes, the egg output can be quantified by using the Kato-Katz technique (20 to 50 mg of fecal material) or the Ritchie technique. Eggs can be found in the urine in infections with "S. haematobium" (recommended time for collection: between noon and 3 PM) and with "S. japonicum". Quantification is possible by using filtration through a nucleopore filter membrane of a standard volume of urine followed by egg counts on the membrane. Tissue biopsy (rectal biopsy for all species and biopsy of the bladder for "S. haematobium") may demonstrate eggs when stool or urine examinations are negative.