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.

"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.

A stool ova and parasites exam reveals the presence of typical whipworm eggs. Typically, the Kato-Katz thick-smear technique is used for identification of the "Trichuris trichiura" eggs in the stool sample.

Although colonoscopy is not typically used for diagnosis, as the adult worms can be overlooked, especially with imperfect colon, there have been reported cases in which colonoscopy has revealed adult worms. Colonoscopy can directly diagnose trichuriasis by identification of the threadlike form of worms with an attenuated, whip-like end. Colonoscopy has been shown to be a useful diagnostic tool, especially in patients infected with only a few male worms and with no eggs presenting in the stool sample.

Trichuriasis can be diagnosed when "T. trichiura" eggs are detected in stool examination. Eggs will appear barrel-shaped and unembryonated, having bipolar plugs and a smooth shell. Rectal prolapse can be diagnosed easily using defecating proctogram and is one of many methods for imaging the parasitic infection. Sigmoidoscopys show characteristic white bodies of adult worms hanging from inflamed mucosa ("coconut cake rectum").

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).

Limited access to essential medicine poses a challenge to the eradication of trichuriasis worldwide. Also, it is a public health concern that rates of post-treatment re-infection need to be determined and addressed to diminish the incidence of untreated re-infection. Lastly, with mass drug administration strategies and improved diagnosis and prompt treatment, detection of an emergence of antihelminthic drug resistance should be examined.

Mass Drug Administration (preventative chemotherapy) has had a positive effect on the disease burden of trichuriasis in East and West Africa, especially among children, who are at highest risk for infection.

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.

Various concentration methods are applied: membrane filter, Knott's concentration method, and sedimentation technique.

Polymerase chain reaction (PCR) and antigenic assays, which detect circulating filarial antigens, are also available for making the diagnosis. The latter are particularly useful in amicrofilaraemic cases. Spot tests for antigen are far more sensitive, and allow the test to be done anytime, rather in the late hours.

Lymph node aspirate and chylous fluid may also yield microfilariae. Medical imaging, such as CT or MRI, may reveal "filarial dance sign" in the chylous fluid; X-ray tests can show calcified adult worms in lymphatics. The DEC provocation test is performed to obtain satisfying numbers of parasites in daytime samples. Xenodiagnosis is now obsolete, and eosinophilia is a nonspecific primary sign.

Filariasis is usually diagnosed by identifying microfilariae on Giemsa stained, thin and thick blood film smears, using the "gold standard" known as the finger prick test. The finger prick test draws blood from the capillaries of the finger tip; larger veins can be used for blood extraction, but strict windows of the time of day must be observed. Blood must be drawn at appropriate times, which reflect the feeding activities of the vector insects. Examples are "W. bancrofti", whose vector is a mosquito; night is the preferred time for blood collection. "Loa loa's" vector is the deer fly; daytime collection is preferred. This method of diagnosis is only relevant to microfilariae that use the blood as transport from the lungs to the skin. Some filarial worms, such as "M. streptocerca" and "O. volvulus", produce microfilarae that do not use the blood; they reside in the skin only. For these worms, diagnosis relies upon skin snips and can be carried out at any time.

If the outbreak is detected early, the organism can be destroyed by quarantines, movement controls, and maybe even put infected animals under euthanasia medication. Tsetse fly populations can be reduced or eliminated by traps, insecticides, and by treating infected animals with antiparasitic drugs. The Tse Tse habitat can be destroyed by alteration of vegetation so they can no longer live there.There are some drugs available that can prevent trypanosomiasis called prophylactic drugs.These drugs are very effective to protect animals during the times they are exposed to challenged diseases. Since they have been around for so long, some were not properly used which caused resistance to these drugs in some places.

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.

Inclusion of NTDs into initiatives for malaria, HIV/AIDS, and tuberculosis, as well as integration of NTD treatment programs, may have advantages given the strong link between these diseases and NTDs. Some neglected tropical diseases share common vectors (sandflies, black flies, and mosquitos). Both medicinal and vector control efforts may be combined.

A four-drug rapid-impact package has been proposed for widespread proliferation. Administration may be made more efficient by targeting multiple diseases at once, rather than separating treatment and adding work to community workers. This package is estimated to cost US$0.40 per patient. When compared to stand-alone treatment, the savings are estimated to be 26–47%. While more research must be done in order to understand how NTDs and other diseases interact in both the vector and the human stages, safety assessments have so far produced positive results.

Many neglected tropical diseases and other prevalent diseases share common vectors, creating another opportunity for treatment and control integration. One such example of this is malaria and lymphatic filariasis. Both diseases are transmitted by the same or related mosquito vectors. Vector control, through the distribution of insecticide treated nets, reduces the human contact with a wide variety of disease vectors. Integrated vector control may also alleviate pressure on mass drug administration, especially with respect to rapidly evolving drug resistance. Combining vector control and mass drug administration deemphasizes both, making each less susceptible to resistance evolution.

The incubation period ranges from 4 days to approximately 8 weeks. The infection leads to significant weight loss and anaemia. Various symptoms are observed, including fever, oedema, adenitis, dermatitis and nervous disorders. The disease cannot be diagnosed with certainty except physically detecting parasites by blood microscopic examination or various serological reactions.

Veterinarians usually attempt diagnosis with skin scrapings from multiple areas, which are then examined under a microscope for mites. "Sarcoptes" mites, because they may be present in relatively low numbers, and because they are often removed by dogs chewing at themselves, may be difficult to demonstrate. As a result, diagnosis in sarcoptic mange is often based on symptoms rather than actual confirmation of the presence of mites. A common and simple way of determining if a dog has mange is if it displays what is called a "pedal-pinna reflex", which is when the dog moves one of its hind legs in a scratching motion as the ear is being manipulated and scratched gently by the examiner; because the mites proliferate on the ear margins in nearly all cases at some point, this method works over 95% of the time. It is helpful in cases where all symptoms of mange are present but no mites are observed with a microscope. The test is also positive in animals with ear mites, an ear canal infection caused by a different but closely related mite (treatment is often the same). In some countries, an available serologic test may be useful in diagnosis.

In laboratory animals, prevention includes a low-stress environment, an adequate amount of nutritional feed, and appropriate sanitation measurements. Because animals likely ingest bacterial spores from contaminated bedding and feed, regular cleaning is a helpful method of prevention. No prevention methods are currently available for wild animal populations.

Affected dogs need to be isolated from other dogs and their bedding, and places they have occupied must be thoroughly cleaned. Other dogs in contact with a diagnosed case should be evaluated and treated. A number of parasitical treatments are useful in treating canine scabies. Sulfurated lime (a mixture of calcium polysulfides) rinses applied weekly or biweekly are effective (the concentrated form for use on plants as a fungicide must be diluted 1:16 or 1:32 for use on animal skin).

Selamectin is licensed for treatment in dogs by veterinary prescription in several countries; it is applied as a dose directly to the skin, once per month (the drug does not wash off). A related and older drug ivermectin is also effective and can be given by mouth for two to four weekly treatments or until two negative skin scrapings are achieved. Oral ivermectin is not safe to use on some collie-like herding dogs, however, due to possible homozygous MDR1 (P-glycoprotein) mutations that increase its toxicity by allowing it into the brain. Ivermectin injections are also effective and given in either weekly or every two weeks in one to four doses, although the same MDR1 dog restrictions apply.

Affected cats can be treated with fipronil and milbemycin oxime.

Topical 0.01% ivermectin in oil (Acarexx) has been reported to be effective in humans, and all mite infections in many types of animals (especially in ear mite infections where the animal cannot lick the treated area), and is so poorly absorbed that systemic toxicity is less likely in these sites. Nevertheless, topical ivermectin has not been well enough tested to be approved for this use in dogs, and is theoretically much more dangerous in zones where the animal can potentially lick the treated area. Selamectin applied to the skin (topically) has some of the same theoretical problems in collies and MDR1 dogs as ivermectin, but it has nevertheless been approved for use for all dogs provided that the animal can be observed for 8 hours after the first monthly treatment. Topical permethrin is also effective in both dogs and humans, but is toxic to cats.

Afoxolaner (oral treatment with a chewable tablet containing afoxolaner 2.27% w/w) has been shown to be efficient against both sarcoptic and demodectic mange in dogs.

Sarcoptic mange is transmissible to humans who come into prolonged contact with infested animals, and is distinguished from human scabies by its distribution on skin surfaces covered by clothing. For treatment of sarcoptic infection in humans, see scabies. For demodetic infection in humans, which is not as severe as it is in animals with thicker coats (such as dogs), see "Demodex folliculorum".

Currently, antibiotic drugs such as penicillin or tetracycline are the only effective methods for disease treatment. Within wild populations, disease control consists of reducing the amount of bacterial spores present in the environment. This can be done by removing contaminated carcasses and scat.

Outbreaks of zoonoses have been traced to human interaction with and exposure to animals at fairs, petting zoos, and other settings. In 2005, the Centers for Disease Control and Prevention (CDC) issued an updated list of recommendations for preventing zoonosis transmission in public settings. The recommendations, developed in conjunction with the National Association of State Public Health Veterinarians, include educational responsibilities of venue operators, limiting public and animal contact, and animal care and management.

Pythiosis is suspected to be heavily underdiagnosed due to unfamiliarity with the disease, the rapid progression and morbidity, and the difficulty in making a diagnosis. Symptoms often appear once the disease has progressed to the point where treatment are less effective.

As the organism is neither a bacterium, virus, nor fungus, routine tests often fail to diagnose it. In cytology and histology, the organism does not stain using Geisma, H&E, or Diff-Quick. GMS staining is required to identify the hyphae in slides. Additionally, the symptoms are usually nonspecific and the disease is not normally included in a differential diagnosis.

Biopsies of infected tissues are known to be difficult to culture, but can help narrow the diagnosis to several different organisms. A definite diagnosis is confirmed using ELISA testing of serum for pythiosis antibodies, or by PCR testing of infected tissues or cultures.

Due to the poor efficacy of single treatments, pythiosis infections are often treated using a variety of different treatments, all with varying success. Most successful treatments include surgery, immunotherapy, and chemotherapy.

Aggressive surgical resection is the treatment of choice for pythiosis. Because it provides the best opportunity for cure, complete excision of infected tissue should be pursued whenever possible. When cutaneous lesions are limited to a single distal extremity, amputation is often recommended. In animals with gastrointestinal pythiosis, segmental lesions should be resected with 5-cm margins whenever possible. Unfortunately, surgical excision of tissue and amputation do not guarantee complete success and lesions can reappear. So, surgery is often followed by other treatments.

An immunotherapy product derived from antigens of "P. insidiosum" has been used successfully to treat pythiosis.

Case reports indicate the use of the following chemotherapy treatments with varying success: potassium iodide, amphotericin B, terbinafine, itraconazole, fluconazole, ketoconazole, natamycin, posaconazole, voriconazole, prednisone, flucytosine, and liposomal nystatin.

Extensive treatments have been used on domestic animals more than on wild animals, probably because infected domestic animals are easier to identify and treat than infected wildlife. Treatment plans and management vary across taxa because this disease tends to affect each species differently. Antifungal drugs are the first line of defense to kill the agents causing phaeohyphomycosis, but despite the significant progress made in the last two decades and a 30% increase in available antifungal drugs since 2000, many drugs are not effective against black fungi. Diseases caused black fungi are hard to treat because the fungi are very difficult to kill. This high resilience may be contributed to the presence of melanin in their cell walls. Current antifungal agents the fungi are not resistant to are posaconazole, voriconazole, and azole isavuconazole.

In 2006, a free-living Eastern box turtle, "Terrapene carolina carolina", was found with a form of phaeohyphomycosis and was brought in the Wildlife Center of Virginia. Its symptom was swelling of the right hindfoot; it was diagnosed as having chromomycosis by histopathology. The center provided a series of antimicrobial treatments and a one-month course of 1 mg itraconazole, administered orally once a day. The eastern box turtle was euthanized due to further complications and the caretakers’ belief that the turtle would not be able to survive if placed back in the wild.

A recent case of a form of phaeohyphomycosis infection was found in a dog in 2011. The Journal of the American Veterinary Medical Association published a case study in which researchers successfully managed an intracranial phaeohyphomycotic fungal granuloma in a one-year-old male Boxer dog. Veterinarians of the Department of Veterinary Clinical Sciences at Tufts University surgically removed the granuloma in the right cerebral hemisphere. The patient was treated with fluconazole for 4 months, and was followed with voriconazole for 10 months. Both are medications used to treat fungal infections. Based on magnetic resonance imaging and cerebrospinal fluid (CSF) analysis 8 months after the surgery, the male Boxer’s outcome was considered excellent.

Emphasis has been placed on how to manage this disease through careful management practices including: proper handling, preventing crowding situation with animals, and transportation. Both the animals and the environment should be treated thoroughly to hinder the spread and control the fungal infection. This is especially important since humans can also contract this disease.

The use of a seven-way clostridial vaccination is the most common, cheapest, and efficacious preventative measure taken against blackleg. Burning the upper layer of soil to eradicate left-over spores is the best way to stop the spread of blackleg from diseased cattle. Diseased cattle should be isolated. Treatment is generally unrewarding due to the rapid progression of the disease, but penicillin is the drug of choice for treatment. Treatment is only effective in the early stages and as a control measure.

Dr. Oliver Morris (O.M.) Franklin made a significant contribution to the welfare of cattle and the livestock industry with his development of the blackleg vaccine. Franklin developed the original method of giving the vaccine while at Kansas State Agriculture College using live cattle. Franklin and another graduate veterinarian founded the original Kansas Blackleg Serum Co. in Wichita in 1916.

Pets can transmit a number of diseases. Dogs and cats are routinely vaccinated against rabies. Pets can also transmit ringworm and "Giardia", which are endemic in both animal and human populations. Toxoplasmosis is a common infection of cats; in humans it is a mild disease although it can be dangerous to pregnant women. Dirofilariasis is caused by "Dirofilaria immitis" through mosquitoes infected by mammals like dogs and cats. Cat-scratch disease is caused by "Bartonella henselae" and "Bartonella quintana" from fleas which are endemic in cats. Toxocariasis is infection of humans of any of species of roundworm, including species specific to the dog ("Toxocara canis)" or the cat ("Toxocara cati"). Cryptosporidiosis can be spread to humans from pet lizards, such as the leopard gecko.

Globally, infants are a population that are especially vulnerable to foodborne disease. The World Health Organization has issued recommendations for the preparation, use and storage of prepared formulas. Breastfeeding remains the best preventative measure for protection of foodborne infections in infants.

Many human diseases can be transmitted to other primates, due to their extensive biological similarities. As a result, centers that hold, treat, or involve close proximity to primates and some other kinds of animals (for example zoos, researchers, and animal hospitals), often take steps to ensure animals are not exposed to human diseases they can catch. In some cases animals are routinely immunized with the same vaccines given to humans.

- Leishmaniasis - Both zoonotic and anthroponotic.

- Influenza, Measles, pneumonia and various other pathogens - Many primates.

- Tuberculosis - Both zoonotic and anthroponotic, with birds, cows, elephants, meerkats, mongooses, monkeys, and pigs known to have been affected.

The term can also be seen in herpetoculture, as this condition can occur in female reptiles. It is inadvisable to attempt to break a reptile egg to remove it from an egg-bound female. This procedure may be done by a veterinarian, who will insert a needle into the egg, and withdraw the contents with a syringe, allowing the egg to collapse and be removed. Non-surgical interventions include administering oxytocin to improve contractions and allow the egg(s) to pass normally. In many cases, egg-bound reptiles must undergo surgery to have stuck eggs removed.

Egg binding in reptiles is quickly fatal if left untreated; therefore, gravid females who become very lethargic and cease feeding need immediate medical treatment in order to treat the potentially life-threatening condition. An episode of the Animal Planet reality show "E-Vet Interns" featured the treatment of an egg-bound turtle named Napoleon. Exotics specialist Dr. Kevin Fitzgerald of Alameda East Veterinary Hospital is shown treating her with oxytocin and then eventually having to resort to surgery with footage of the large number of eggs that were removed. Dr. Fitzgerald was shown explaining to the new interns how dangerous this condition can be for a pet turtle and the need for early veterinary intervention.

Egg binding can occur if an egg is malformed and/or too large, the animal is weakened by illness, improper husbandry, stress, or if hormonal balances are wrong (producing weak contractions). Factors that can contribute to the risk of egg binding include calcium deficiency, breeding animals that are too young or too small, not providing suitable laying areas (leading to deliberate retention of eggs), and overfeeding of species in which clutch size is dependent on food intake (such as Veiled Chameleons).

In the context of behavioral ecology, egg binding can be an important factor in limiting clutch size. Lizards that lay fewer, but larger eggs are at higher risk for egg binding, and so there is selection pressure towards a minimum clutch size. For example, in common side-blotched lizards, females that lay fewer than the average 4–5 eggs per clutch have significantly increased risk of egg binding.

Diagnosis is most commonly done with the identification of bacteria in the lesions by a microscope observation. Ticks, biting flies, and contact with other infected animals also causes the spread of rainscald. A scab will be taken from the affected animal and stained so that the bacteria are visible under a microscope inspection. A positive diagnosis of rainscald can be confirmed if filamentous bacteria are observed with as well as chains of small, spherical bacteria. If a diagnosis cannot be confirmed with a microscope, blood agar cultures can be grown to confirm the presence of "D. congolensis". The resulting colonies have filaments and are yellow in colour.