Contact with farm animals can lead to disease in farmers or others that come into contact with infected animals. Glanders primarily affects those who work closely with horses and donkeys. Close contact with cattle can lead to cutaneous anthrax infection, whereas inhalation anthrax infection is more common for workers in slaughterhouses, tanneries and wool mills. Close contact with sheep who have recently given birth can lead to clamydiosis, or enzootic abortion, in pregnant women, as well as an increased risk of Q fever, toxoplasmosis, and listeriosis in pregnant or the otherwise immunocompromised. Echinococcosis is caused by a tapeworm which can be spread from infected sheep by food or water contaminated with feces or wool. Bird flu is common in chickens. While rare in humans, the main public health worry is that a strain of bird flu will recombine with a human flu virus and cause a pandemic like the 1918 Spanish flu. In 2017, free range chickens in the UK were temporarily ordered to remain inside due to the threat of bird flu. Cattle are an important reservoir of cryptosporidiosis and mainly affects the immunocompromised.

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.

Rocky Mountain spotted fever, like all rickettsial infections, is classified as a zoonosis. Zoonoses are diseases of animals that can be transmitted to humans. Some zoonotic diseases require a vector (e.g., a mosquito, tick, or flea) to be transmitted from the animal host to the human host. In the case of Rocky Mountain spotted fever, ticks are the natural hosts, serving as both reservoirs and vectors of "R. rickettsii". Ticks transmit the organism to vertebrates primarily by their bites. Less commonly, infections may occur following exposure to crushed tick tissues, fluids, or tick feces.

A female tick can transmit "R. rickettsii" to her eggs in a process called transovarial transmission. Ticks can also become infected with "R. rickettsii" while feeding on blood from the host in either the larval or nymphal stage. After the tick develops into the next stage, the "R. rickettsii" may be transmitted to the second host during the feeding process. Furthermore, male ticks may transfer "R. rickettsii" to female ticks through body fluids or spermatozoa during the mating process. These types of transmission represent how generations or life stages of infected ticks are maintained. Once infected, the tick can carry the pathogen for life.

Rickettsiae are transmitted to a vertebrate host through saliva while a tick is feeding. It usually takes about 24 hours of attachment and feeding before the rickettsiae are transmitted to the host. In general, about one to three percent of the tick population carries "R. rickettsii", even in areas where the majority of human cases are reported. Therefore, the risk of exposure to a tick carrying "R. rickettsii" is low.

Vectors include the American dog tick "Dermacentor variabilis", "Dermacentor andersoni", "Rhipicephalus sanguineus", and "Amblyomma cajennense". Not all of these are of equal importance, and most are restricted to certain geographic areas.

The two major vectors of "R. rickettsii" in the United States are the American dog tick (Dermacentor variabilis) and the Rocky Mountain wood tick (Dermacentor andersoni). American dog ticks are widely distributed east of the Rocky Mountains and they also occur in limited areas along the Pacific Coast. Dogs and medium-sized mammals are the preferred hosts of an adult American dog ticks, although it feeds readily on other large mammals, including human beings. This tick is the most commonly identified species responsible for transmitting "R. rickettsii" to humans. Rocky Mountain wood ticks ("Dermacentor andersoni") are found in the Rocky Mountain states and in southwestern Canada. The life cycle of this tick may require up to three years for its completion. The adult ticks feed primarily on large mammals. The larvae and nymphs feed on small rodents.

Other tick species have been shown to be naturally infected with "R. rickettsii" or serve as experimental vectors in the laboratory. These species are likely to play only a minor role in the ecology of "R. rickettsii".

Rocky Mountain spotted fever can be a very severe illness and patients often require hospitalization. Because "R. rickettsii" infects the cells lining blood vessels throughout the body, severe manifestations of this disease may involve the respiratory system, central nervous system, gastrointestinal system, or kidneys.

Long-term health problems following acute Rocky Mountain spotted fever infection include partial paralysis of the lower extremities, gangrene requiring amputation of fingers, toes, or arms or legs, hearing loss, loss of bowel or bladder control, movement disorders, and language disorders. These complications are most frequent in persons recovering from severe, life-threatening disease, often following lengthy hospitalizations

For infecting organisms to survive and repeat the infection cycle in other hosts, they (or their progeny) must leave an existing reservoir and cause infection elsewhere. Infection transmission can take place via many potential routes:

- Droplet contact, also known as the "respiratory route", and the resultant infection can be termed airborne disease. If an infected person coughs or sneezes on another person the microorganisms, suspended in warm, moist droplets, may enter the body through the nose, mouth or eye surfaces.

- Fecal-oral transmission, wherein foodstuffs or water become contaminated (by people not washing their hands before preparing food, or untreated sewage being released into a drinking water supply) and the people who eat and drink them become infected. Common fecal-oral transmitted pathogens include "Vibrio cholerae", "Giardia" species, rotaviruses, "Entameba histolytica", "Escherichia coli", and tape worms. Most of these pathogens cause gastroenteritis.

- Sexual transmission, with the resulting disease being called sexually transmitted disease

- Oral transmission, Diseases that are transmitted primarily by oral means may be caught through direct oral contact such as kissing, or by indirect contact such as by sharing a drinking glass or a cigarette.

- Transmission by direct contact, Some diseases that are transmissible by direct contact include athlete's foot, impetigo and warts

- Vehicle Transmission, transmission by an inanimate reservoir (food, water, soil).

- Vertical transmission, directly from the mother to an embryo, fetus or baby during pregnancy or childbirth. It can occur when the mother gets an infection as an intercurrent disease in pregnancy.

- Iatrogenic transmission, due to medical procedures such as injection or transplantation of infected material.

- Vector-borne transmission, transmitted by a vector, which is an organism that does not cause disease itself but that transmits infection by conveying pathogens from one host to another.

The relationship between "virulence versus transmissibility" is complex; if a disease is rapidly fatal, the host may die before the microbe can be passed along to another host.

Infectious diseases are sometimes called contagious disease when they are easily transmitted by contact with an ill person or their secretions (e.g., influenza). Thus, a contagious disease is a subset of infectious disease that is especially infective or easily transmitted. Other types of infectious/transmissible/communicable diseases with more specialized routes of infection, such as vector transmission or sexual transmission, are usually not regarded as "contagious", and often do not require medical isolation (sometimes loosely called quarantine) of victims. However, this specialized connotation of the word "contagious" and "contagious disease" (easy transmissibility) is not always respected in popular use.

Infectious diseases are commonly transmitted from person to person through direct contact. The types of contact are through person to person and droplet spread. Indirect contact such as airborne transmission, contaminated objects, food and drinking water, animal person contact, animal reservoirs, insect bites, and environmental reservoirs are another way infectious diseases are transmitted,

Bacteria are a common cause of foodborne illness. In the United Kingdom during 2000, the individual bacteria involved were the following: "Campylobacter jejuni" 77.3%, "Salmonella" 20.9%, 1.4%, and all others less than 0.56%. In the past, bacterial infections were thought to be more prevalent because few places had the capability to test for norovirus and no active surveillance was being done for this particular agent. Toxins from bacterial infections are delayed because the bacteria need time to multiply. As a result, symptoms associated with intoxication are usually not seen until 12–72 hours or more after eating contaminated food. However, in some cases, such as Staphylococcal food poisoning, the onset of illness can be as soon as 30 minutes after ingesting contaminated food.

Most common bacterial foodborne pathogens are:

- "Campylobacter jejuni" which can lead to secondary Guillain–Barré syndrome and periodontitis

- "Clostridium perfringens", the "cafeteria germ"

- "Salmonella" spp. – its "S. typhimurium" infection is caused by consumption of eggs or poultry that are not adequately cooked or by other interactive human-animal pathogens

- "" enterohemorrhagic (EHEC) which can cause hemolytic-uremic syndrome

Other common bacterial foodborne pathogens are:

- "Bacillus cereus"

- "Escherichia coli", other virulence properties, such as enteroinvasive (EIEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enteroaggregative (EAEC or EAgEC)

- "Listeria monocytogenes"

- "Shigella" spp.

- "Staphylococcus aureus"

- "Staphylococcal enteritis"

- "Streptococcus"

- "Vibrio cholerae", including O1 and non-O1

- "Vibrio parahaemolyticus"

- "Vibrio vulnificus"

- "Yersinia enterocolitica" and "Yersinia pseudotuberculosis"

Less common bacterial agents:

- "Brucella" spp.

- "Corynebacterium ulcerans"

- "Coxiella burnetii" or Q fever

- "Plesiomonas shigelloides"

Viral infections make up perhaps one third of cases of food poisoning in developed countries. In the US, more than 50% of cases are viral and noroviruses are the most common foodborne illness, causing 57% of outbreaks in 2004. Foodborne viral infection are usually of intermediate (1–3 days) incubation period, causing illnesses which are self-limited in otherwise healthy individuals; they are similar to the bacterial forms described above.

- Enterovirus

- Hepatitis A is distinguished from other viral causes by its prolonged (2–6 week) incubation period and its ability to spread beyond the stomach and intestines into the liver. It often results in jaundice, or yellowing of the skin, but rarely leads to chronic liver dysfunction. The virus has been found to cause infection due to the consumption of fresh-cut produce which has fecal contamination.

- Hepatitis E

- Norovirus

- Rotavirus

The hepatitis E virus causes around 20 million infections a year. These result in around three million acute illnesses and as of 2010, 57,000 deaths annually. It is particularly dangerous for pregnant women, who can develop an acute form of the disease that is lethal in 30% of cases or more. HEV is a major cause of illness and of death in the developing world and disproportionate cause of deaths among pregnant women. Hepatitis E is endemic in Central Asia, while Central America and the Middle East have reported outbreaks.

Sanitation is the most important measure in prevention of hepatitis E; this consists of proper treatment and disposal of human waste, higher standards for public water supplies, improved personal hygiene procedures, and sanitary food preparation. Thus, prevention strategies of this disease are similar to those of many others that plague developing nations.

Another human health issue caused by animal hoarding is the risk of zoonotic diseases. Defined as "human diseases acquired from or transmitted to any other vertebrate animal", zoonotic diseases can often be lethal and in all cases constitute a serious public health concern. Examples of well-known zoonotic diseases include bubonic plague, influenza, and rabies. Common domesticated animals constitute a large portion of animals carrying zoonoses, and as a result, humans involved in animal hoarding situations are at particular risk of contracting disease. Zoonoses that may arise in hoarding situations—through vectors such as dog, cat, or rat bites—include rabies, salmonellosis, catscratch fever, hookworm, and ringworm. One zoonosis of special concern is toxoplasmosis, which can be transmitted to humans through cat feces or badly-prepared meat, and is known to cause severe birth defects or stillbirth in the case of infected pregnant women. The risk of zoonotic diseases is amplified by the possibility of community epidemics.

Animal hoarding also causes many health problems for the people involved. Hoarders, by definition, fail to correct the deteriorating sanitary conditions of their living spaces, and this gives rise to several health risks for those living in and around hoarding residences. Animal hoarding is at the root of a string of human health problems including poor sanitation, fire hazards, zoonotic diseases, envenomation, and neglect of oneself and dependents.

Spondylodiscitis is the most common complication of sepsis or local infection, usually in the form of an abscess. The main causative organisms are staphylococci and Mycobacterium tuberculosis, but potential organisms include a large number of bacteria, fungi, zoonoses. Spondylodiscitis frequently develops in immunocompromised individuals, such as by a cancer, infection, or by immunosuppressive drugs used for organ transplantations.

Spondylodiscitis is a combination of discitis (inflammation of one or more intervertebral disc spaces) and spondylitis (inflammation of one or more vertebrae), the latter generally involving the areas adjacent to the intervertebral disc space.

Zoophilia is a paraphilia involving a sexual fixation on non-human animals. Bestiality is cross-species sexual activity between human and non-human animals. The terms are often used interchangeably, but some researchers make a distinction between the attraction (zoophilia) and the act (bestiality).

Although sex with animals is not outlawed in some countries, in most countries, bestiality is illegal under animal abuse laws or laws dealing with buggery or crimes against nature.

Infections that are transmitted from animals to humans are called zoonoses. Some zoonoses may be transferred through casual contact, but others are much more readily transferred by activities that expose humans to the semen, vaginal fluids, urine, saliva, feces and blood of animals. Examples of zoonoses are Brucellosis, Q fever, leptospirosis, and toxocariasis. Therefore, sexual activity with animals is, in some instances, a high risk activity. Allergic reactions to animal semen may occur, including anaphylaxis. Bites and other trauma from penetration or trampling may occur.