Coccidiosis is a significant disease for chickens, especially affecting the young chicks. It can be fatal or leave the bird with compromised digestion. There are chick feed mixes that contain a coccidiostat to manage exposure levels and control disease. In an outbreak, coccidiocidal medications are given. Examples are toltrazuril (Baycox) or amprolium. After multiple infections, surviving chickens become resistant to the coccidia.

The most common medications used to treat coccidian infections are in the sulfonamide antibiotic family.

Depending on the pathogen and the condition of the animal, untreated coccidiosis may clear of its own accord, or become severe and damaging, and sometimes cause death.

Histomoniasis (or histomonosis), also known as blackhead disease, is a commercially important disease of poultry, particularly of chickens and turkeys, due to parasitic infection of a protozoan, "Histomonas meleagridis". The protozoan is transmitted to the bird by the nematode parasite "Heterakis gallinarum". "H. meleagridis" resides within the eggs of "H. gallinarum", so birds ingest the parasites along with contaminated soil or food. Earthworms can also act as a paratenic host.

"Histomonas meleagridis" specifically infects the cecum and liver. Symptoms of the infection include depression, reduced appetite, poor growth, increased thirst, sulphur-yellow diarrhoea, listlessness, and dry, ruffled feathers. The head may become cyanotic (bluish in colour), hence the common name of the disease, blackhead disease; thus the name 'blackhead' is in all possibility a misnomer for discoloration. The disease carries a high mortality rate, and is particularly highly fatal in poultry, and less in other birds. Currently, no prescription drug is available to treat this disease.

Poultry (especially free-ranging) and wild birds commonly harbor a number of parasitic worms with only mild health problems from them. Turkeys are much more susceptible to getting blackhead than are chickens. Thus, chickens can be infected carriers for a long time because they are not removed or medicated by their owners, and they do not die or stop eating/defecating. "H. gallinarum" eggs can remain infective in soil for four years, a high risk of transmitting blackhead to turkeys remains if they graze areas with chicken feces in this time frame.

Because of Eustrongylides species’ complex life cycle with various host species, preventing infection and controlling outbreaks is difficult. Outbreaks of this disease are closely linked to agricultural runoff and urban development Eutrophication of water bodies supports high population levels of oligochaete worms, which causes increased numbers of infected fish that eat the worms, and then the birds who eat the fish.

One way to prevent Eustrongylidosis is to control oligochaete populations. Outbreaks of this parasite are closely linked to high numbers of oligochaete worms in the area’s waterways. This is because the worms are essential for Eustrongylides species to reproduce. Oligochaete populations can be controlled by monitoring nutrient levels in the water, because high nutrient levels support oligochaete populations. They can also be controlled by decreasing the level of oxygen in the water. Encouraging responsible farming practices in order to reduce chemical run-off will help prevent this disease from occurring.

Managers need to be diligent in catching the symptoms of the parasite before it can become an outbreak. Once an outbreak of Eustrongylidosis has occurred, there is little that ecosystem managers can do to stop the spread in oligochaetes, fish and birds. Traditional anthelminthics (dewormers) are not effective in fish because they kill parasites that live inside the gastrointestinal tract, whereas Eustrongylides species live outside the stomach in the body cavity. The parasites can only be removed from fish surgically, which is not feasible. In order to completely stop the Eustrongylides life cycle in fish, all fish in an affected area must be culled.

Surgical removal of the parasite from wading birds is a viable option, but this would also not be feasible for a large number of birds, and it would not stop the cycle of infection.

Currently, no therapeutic drugs are prescribed for the disease. Therefore, prevention is the sole mode of treatment. This disease can only be prevented by quarantining sick birds and preventing migration of birds around the house, causing them to spread the disease. Deworming of birds with anthelmintics can reduce exposure to the cecal nematodes that carry the protozoan. Good management of the farm, including immediate quarantine of infected birds and sanitation, is the main useful strategy for controlling the spread of the parasitic contamination. The only drug used for the control (prophylaxis) in the United States is nitarsone at 0.01875% of feed until 5 days before marketing. Natustat and nitarsone were shown to be effective therapeutic drugs. Nifurtimox, a compound with known antiprotozoal activity, was demonstrated to be significantly effective at 300–400 ppm, and well tolerated by turkeys.

Eustrongylidosis is a parasitic disease that mainly affects wading birds worldwide; however, the parasite’s complex, indirect life cycle involves other species such as aquatic worms and fish. Moreover, this disease is zoonotic which means the parasite can transmit disease from animals to humans. Eustrongylidosis is named after the causative agent Eustrongylides and typically occurs in eutrophicated waters where concentrations of nutrients and minerals are high enough to provide ideal conditions for the parasite to thrive and persist. Because eutrophication has become a common issue due to agricultural runoff and urban development, cases of Eustrongylidosis are becoming prevalent and hard to control. Eustrongylidosis can be diagnosed before or after death by observing behavior, clinical signs and performing fecal flotations and necropsies. Methods to control Eustrongylidosis include preventing eutrophication and providing hosts with uninfected food sources in aquaculture farms. Parasites are known to be indicators of environmental health and stability and should therefore be studied further to better understand the parasite’s life cycle and how it affects predator-prey interactions and improve conservation efforts.

Avian malaria is most notably caused by Plasmodium relictum, a protist that infects birds in all parts of the world apart from Antarctica. There are several other species of "Plasmodium" that infect birds, such as "Plasmodium anasum" and "Plasmodium gallinaceum", but these are of less importance except, in occasional cases, for the poultry industry. The disease is found worldwide, with important exceptions. Usually, it does not kill birds. However, in areas where avian malaria is newly introduced, such as the islands of Hawaiʻi, it can be devastating to birds that have lost evolutionary resistance over time.

Avian malaria is a parasitic disease of birds, caused by parasite species belonging to the genera "Plasmodium" and "Hemoproteus" (phylum Apicomplexa, class Haemosporidia, family Plasmoiidae). The disease is transmitted by a dipteran vector including mosquitoes in the case of "Plasmodium" parasites and biting midges for "Hemoproteus." The range of symptoms and effects of the parasite on its bird hosts is very wide, from asymptomatic cases to drastic population declines due to the disease, as is the case of the Hawaiian honeycreepers. The diversity of parasites is large, as it is estimated that there are approximately as many parasites as there are species of hosts. Co-speciation and host switching events have contributed to the broad range of hosts that these parasites can infect, causing avian malaria to be a widespread global disease, found everywhere except Antarctica.

Diagnosis is made with isolation of "Pasteurella multocida" in a normally sterile site (blood, pus, or cerebrospinal fluid).

As the infection is usually transmitted into humans through animal bites, antibiotics usually treat the infection, but medical attention should be sought if the wound is severely swelling. Pasteurellosis is usually treated with high-dose penicillin if severe. Either tetracycline or chloramphenicol provides an alternative in beta-lactam-intolerant patients. However, it is most important to treat the wound.

Streptococcus species are the cause of opportunistic infections in poultry leading to acute and chronic conditions in affected birds. Disease varies according to the Streptococcal species but common presentations include septicaemia, peritonitis, salpingitis and endocarditis.

Common species affecting poultry include:

- "S. gallinaceus" in broiler chickens

- "S. gallolyticus" which is a pathogen of racing pigeons and turkey poults

- "S. dysgalactiae" in broiler chickens

- "S. mutans" in geese

- "S. pluranimalium" in broiler chickens

- "S. equi subsp. zooepidemicus" in chickens and turkeys

- "S. suis" in psittacine birds

The organism should be cultured and antibiotic sensitivity should be determined before treatment is started. Amoxycillin is usually effective in treating streptococcal infections.

Biosecurity protocols and good hygiene are important in preventing the disease.

Vaccination is available against "S. gallolyticus" and can also protect pigeons.

In birds, "Chlamydia psittaci" infection is referred to as avian chlamydiosis (AC). Infected birds shed the bacteria through feces and nasal discharges, which can remain infectious for several months. Many strains remain quiescent in birds until activated under stress. Birds are excellent, highly mobile vectors for the distribution of chlamydial infection because they feed on, and have access to, the detritus of infected animals of all sorts.

Prevention is through use of Stock coryza-free birds. In other areas culling of the whole flock is a good means of the disease control. Bacterin also is used at a dose of two to reduce brutality of the disease. Precise exposure has also has been used but it should be done with care. Vaccination of the chicks is done in areas with high disease occurrence. Treatment is done by using antibiotics such as erythromycin, Dihydrostreptomycin, Streptomycin sulphonamides, tylosin and Flouroquinolones .

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.

In sheep, the disease is also called the "circling disease". The most obvious signs for the veterinarians are neurological, especially lateral deviation of the neck and head.

Scaly leg is a disease of chickens and other birds. It is caused by a parasitic mite, "cnemidocoptes mutans". The mite burrows under the scales in the bird's legs, but may also infest other areas, such as the comb or wattles of chickens. The mite spends its entire lifecycle on the birds and is usually spread by direct contact.

Birds infested with scaly leg have raised or protruding scales, sometimes with a white crusty appearance. Scaly leg is irritating to the infected bird, and in extreme cases can result in lameness.

In domestic birds the disease may be treated by application of an oily substance such as petroleum jelly, vegetable oil, or a commercial chest rub, thus preventing the mites breathing. Alternatively an insecticide may be used to kill the mites – or the two methods may be combined. The loose crusty scales may also be removed by soaking the afflicted bird's legs in soapy water mixed with diluted ammonia, and the encrusted areas scrubbed gently with a soft brush. Complete removal may take multiple treatments. Dropped scales may remain infectious for up to a month, and so pen, perches, and nesting areas may also be treated, or birds may be moved to different housing for several weeks.

MAP is capable of causing Johne's-like symptoms in humans, though difficulty in testing for MAP infection presents a diagnostic hurdle.

Clinical similarities are seen between Johne's disease in ruminants and inflammatory bowel disease in humans, and because of this, some researchers contend the organism is a cause of Crohn's disease. However, epidemiologic studies have provided variable results; in certain studies, the organism (or an immune response directed against it) has been much more frequently found in patients with Crohn's disease than asymptomatic people.

"C. psittaci" in birds is often systemic and infections can be inapparent, severe, acute or chronic with intermittent shedding. Signs in birds include "inflamed eyes, difficulty in breathing, watery droppings and green urates."

The reservoirs of the disease are carrier chickens which could be health but harboring the disease or chronically sick chickens. The disease affects all ages of chickens. The disease can persist in the flock for 2-3 weeks and signs of the disease are seen between 1–3 days post infection. Transmission of the disease is through direct interaction, airborne droplets and drinking contaminated water. Chicken having infection and those carriers contribute highly to the disease transmission

In an endemic herd, only a minority of the animals develops clinical signs; most animals either eliminate the infection or become asymptomatic carriers. The mortality rate is about 1%, but up to 50% of the animals in the herd can be asymptomatically infected, resulting in losses in production. Once the symptoms appear, paratuberculosis is progressive and affected animals eventually die. The percentage of asymptomatic carriers that develop overt disease is unknown.

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.

Inactivated vaccines may control the disease, but will not cure it.

Phaeohyphomycosis is a heterogeneous group of mycotic infections caused by dematiaceous fungi whose morphologic characteristics in tissue include hyphae, yeast-like cells, or a combination of these. It can be associated an array of darkly-pigmented hyphomycetes including "Alternaria" species"," "Exophiala jeanselmei," and "Rhinocladiella mackenziei".

The term “phaeohyphomycosis” was introduced to determine infections caused by dematiaceous or pigmented filamentous fungi which contain melanin in their cell walls. Phaeohyphomycosis is an uncommon infection, however the number of case reported has been increasing in recent years. The presence of melanin in cell walls may be a virulence factor for the pathogens caused by the fungi. The outcome of antifungal treatment is poor, and mortality is almost 80%. Phaeohyphomycosis has been attributed to more than 100 species and 60 genera of fungi over the past several decades. The pathogens are considered opportunistic. Almost all cases of widely disseminated infection have occurred in immunosuppressed patients.

Listeriosis is an infectious but not contagious disease caused by the bacterium "Listeria monocytogenes", far more common in domestics animals (domestic mammals and poultry), especially ruminants, than in human beings. It can also occur in feral animals—among others, game animals—as well as in poultry and other birds.

The causative bacterium lives in the soil and in poorly made silage, and is acquired by ingestion. It is not contagious; over the course of a 30-year observation period of sheep disease in Morocco, the disease only appeared in the late 2000s (decade) when feeding bag-ensiled corn became common. In Iceland, the disease is called "silage sickness".

The disease is sporadic, but can occur as farm outbreaks in ruminants.

Three main forms are usually recognized throughout the affected species:

- encephalitis, the most common form in ruminants

- late abortion

- gastro-intestinal septicemia with liver damage, in monogastric species as well as in preruminant calves and lambs

Listeriosis in animals can sometimes be cured with antibiotics (tetracyclines, chloramphenicol and benzyl penicillin) when diagnosed early. Goats, for example, can be treated upon first noticing the disease's characteristic expression in the animal's face, but is generally fatal.