Researchers have published conflicting reports concerning whether "Blastocystis" causes symptoms in humans, with one of the earliest reports in 1916. The incidence of reports associated with symptoms began to increase in 1984, with physicians from Saudi Arabia reporting symptoms in humans and US physicians reporting symptoms in individuals with travel to less developed countries. A lively debate ensued in the early 1990s, with some physicians objecting to publication of reports that "Blastocystis" caused disease. Some researchers believe the debate has been resolved by finding of multiple species of "Blastocystis" that can infect humans, with some causing symptoms and others being harmless (see Genetics and Symptoms).

A few of most commonly reported symptoms are:

- abdominal pain

- itching, usually anal itching

- constipation

- diarrhea

- watery or loose stools

- weight loss

- fatigue

- flatulence

Some less commonly reported symptoms include:

- Skin rash

- Headache, depression

- Arthritic symptoms and joint pain

- Intestinal inflammation

There are conflicting reports regarding whether "Blastocystis" causes disease in humans. These reports resulted in a brief debate in medical journals in the early 1990s between some physicians in the United States who believed that "Blastocystis" was harmless, and physicians in the United States and overseas who believed it could cause disease.

At the time, it was common practice to identify all "Blastocystis" from humans as "Blastocystis hominis", while "Blastocystis" from animals was identified differently (e.g. "Blastocystis ratti" from rats). Research performed since then has shown that the concept of "Blastocystis hominis" as a unique species of "Blastocystis" infecting humans is not supported by microbiological findings. Although one species group associated with primates was found, it was also discovered that humans can acquire infection from any one of nine species groups of "Blastocystis" which are also carried by cattle, pigs, rodents, chickens, pheasants, monkeys, dogs and other animals. Research has suggested that some types produce few or no symptoms, while others producing illness and intestinal inflammation. Researchers have suggested conflicting reports may be due to the practice of naming all "Blastocystis" from humans "Blastocystis hominis" and have proposed discontinuing the use of that term.

A standard naming system for "Blastocystis" organisms from humans and animals has been proposed which names "Blastocystis" isolates according to the genetic identity of the "Blastocystis" organism rather than the host. The naming system used identifies all isolates as "Blastocystis sp. subtype nn" where nn is a number from 1 to 9 indicating the species group of the "Blastocystis" organism. The identification of the species can not be performed with a microscope at this time, because the different species look alike. Identification requires equipment for genetic analysis that is common in microbiology laboratories, but not available to most physicians. Some new scientific papers have begun using the standard naming system.

Common signs and symptoms of intestinal cryptosporidiosis include:

- Moderate to severe watery diarrhea, sometimes contains mucus and rarely contains blood or leukocytes

- In very severe cases, diarrhea may be profuse and cholera-like with malabsorption and hypovolemia

- Low-grade fever

- Crampy abdominal pain

- Dehydration

- Weight loss

- Fatigue

- Nausea and vomiting – suggests upper GI tract involvement and may lead to respiratory cryptosporidiosis

- Epigastric or right upper quadrant tenderness

Less common or rare signs and symptoms include:

- Reactive arthritis (may affect the hands, knees, ankles, and feet)

- Jaundice – suggests hepatobiliary involvement

- Ascites – suggests pancreatic involvement

Symptoms of upper respiratory cryptosporidiosis include:

- Inflammation of the nasal mucosa, sinuses, larynx, or trachea

- Nasal discharge

- Voice change (e.g., hoarseness)

Symptoms of lower respiratory cryptosporidiosis include:

- Cough

- Shortness of breath

- Fever

- Hypoxemia

The average incubation periods for giardiasis and cryptosporidiosis are each 7 days. Certain other bacterial and viral agents have shorter incubation periods, although hepatitis may take weeks to manifest itself. The onset usually occurs within the first week of return from the field, but may also occur at any time while hiking.

Most cases begin abruptly and usually result in increased frequency, volume, and weight of stool. Typically, a hiker experiences at least four to five loose or watery bowel movements each day. Other commonly associated symptoms are nausea, vomiting, abdominal cramping, bloating, low fever, urgency, and malaise, and usually the appetite is affected. The condition is much more serious if there is blood or mucus in stools, abdominal pain, or high fever. Dehydration is a possibility. Life-threatening illness resulting from WAD is extremely rare but can occur in people with weakened immune systems.

Some people may be carriers and not exhibit symptoms.

Adult flukes are known to be quite harmless, as they do not attack on the host tissue. It is the immature flukes which are most damaging as they get attached to the intestinal wall, literally and actively sloughing off of the tissue. This necrosis is indicated by haemorrhage in faeces, which in turn is a sign of severe enteritis. Under such condition the animals become anorexic and lethargic. It is often accompanied by pronounced diarrhoea, dehydration, oedema, polydipsia, anaemia, listlessness and weight loss. In sheep profuse diarrhoea usually develops two to four weeks after initial infection. If infection is not properly attended death can ensue within 20 days, and in a farm mortality can be very high. In fact there are intermittent reports of mortality as high as 80% among sheep and cattle. Sometimes chronic form is also seen with severe emaciation, anaemia, rough coat, mucosal oedema, thickened duodenum and oedema in the sub maxillary space. The terminally sick animals lie prostrate on the ground, completely emaciated until they die. In buffalos, severe haemorrhage was found to be associated with liver cirrhosis and nodular hepatitis.

Amphistomiasis or paramphistomiasis (alternatively spelled amphistomosis or paramphistomosis) is a parasitic disease of livestock animals, more commonly of cattle and sheep, and humans caused by immature helminthic flatworms belonging to the order Echinostomida. The term amphistomiasis is used for broader connotation implying the disease inflicted by members of Echinostomida including the family Paramphistomidae/Gastrodiscidae (to be precise, the species "Gastrodiscoides hominis"); whereas paramphistomiasis is restricted to that of the members of the family Paramphistomatidae only. "G. discoides" and "Watsonius watsoni" are responsible for the disease in humans, while most paramphistomes are responsible in livestock animals, and some wild mammals. In livestock industry the disease causes heavy economic backlashes due to poor production of milk, meat and wool.

Diarrhea acquired in the wilderness or other remote areas is typically a form of infectious diarrhea, itself classified as a type of secretory diarrhea. These are all considered forms of gastroenteritis. The term may be applied in various remote areas of non-tropical developed countries (U.S., Canada, western Europe, etc.), but is less applicable in developing countries, and in the tropics, because of the different pathogens that are most likely to cause infection.

Signs and symptoms of enteritis are highly variable and vary based on the specific cause and other factors such as individual variance and stage of disease.

Symptoms may include abdominal pain, cramping, diarrhoea, dehydration, fever, nausea, vomiting and weight loss.

Microsporidiosis is an opportunistic intestinal infection that causes diarrhea and wasting in immunocompromised individuals (HIV, for example). It results from different species of microsporidia, a group of microbial (unicellular) fungi.

In HIV infected individuals, microsporidiosis generally occurs when CD4+ T cell counts fall below 150.

A sharp rise in mortality is often seen (depending on the virulence of the disease). Other clinical signs include abdominal swelling, anorexia, abnormal swimming, darkening of the skin, and trailing of the feces from the vent. On necropsy, internal damage (viral necrosis) to the pancreas and thick mucus in the intestines often is present. Surviving fish should recover within one to two weeks.

Diagnostic methods for the detection of the disease include: characteristic histological pancreatic lesion, PCR, indirect fluorescent antibody testing, ELISA, and virus culture. High virus titers can be isolated from carrier animals.

The symptoms of an infection depend on the type of disease. Some signs of infection affect the whole body generally, such as fatigue, loss of appetite, weight loss, fevers, night sweats, chills, aches and pains. Others are specific to individual body parts, such as skin rashes, coughing, or a runny nose.

In certain cases, infectious diseases may be asymptomatic for much or even all of their course in a given host. In the latter case, the disease may only be defined as a "disease" (which by definition means an illness) in hosts who secondarily become ill after contact with an asymptomatic carrier. An infection is not synonymous with an infectious disease, as some infections do not cause illness in a host.

Enterocolitis or coloenteritis is an inflammation of the digestive tract, involving enteritis of the small intestine and colitis of the colon. It may be caused by various infections, with bacteria, viruses, fungi, parasites, or other causes. Common clinical manifestations of enterocolitis are frequent diarrheal defecations, with or without nausea, vomiting, abdominal pain, fever, chills, alteration of general condition. General manifestations are given by the dissemination of the infectious agent or its toxins throughout the body, or – most frequently – by significant losses of water and minerals, the consequence of diarrhea and vomiting.

Among the causal agents of acute enterocolitis are:

- bacteria: "Salmonella", "Shigella", "Escherichia coli", "Campylobacter" etc.;

- viruses: enteroviruses, rotaviruses, Norwalk virus, adenoviruses;

- fungi: candidiasis, especially in immunosuppressed patients or who have previously received prolonged antibiotic treatment;

- parasites: "Giardia lamblia" (with high frequency of infestation in the population, but not always with clinical manifestations), "Balantidium coli", "Blastocystis homnis", "Cryptosporidium" (diarrhea in people with immunosuppression), "Entamoeba histolytica" (produces the amebian dysentery, common in tropical areas).

Although it is classified as a protozoal disease in ICD-10, their phylogenetic placement has been resolved to be within the Fungi, and some sources classify microsporidiosis as a mycosis, however, they are highly divergent and rapidly evolving.

Infectious pancreatic necrosis (IPN) is a severe viral disease of salmonid fish. It is caused by infectious pancreatic necrosis virus, which is a member of the Birnaviridae family. This disease mainly affects young salmonids, such as trout or salmon, of less than six months, although adult fish may carry the virus without showing symptoms. Resistance to infection develops more rapidly in warmer water. It is highly contagious and found worldwide, but some regions have managed to eradicate or greatly reduce the incidence of disease. The disease is normally spread horizontally via infected water, but spread also occurs vertically. It is not a zoonosis.

Flacherie (literally: "flaccidness") is a disease of silkworms, caused by silkworms eating infected or contaminated mulberry leaves. Flacherie infected silkworms look weak and can die from this disease. Silkworm larvae that are about to die from Flacherie are a dark brown.

There are two kinds of flacherie: essentially, infectious (viral) flacherie and noninfectious ("bouffee") flacherie. Both are technically a lethal diarrhea.

Bouffée flacherie is caused by heat waves ("bouffée" means "sudden heat spell" in French).

Viral flacherie is ultimately caused by infection with "Bombyx mori" infectious flacherie virus (BmIFV, Iflaviridae), "Bombyx mori" densovirus (BmDNV, Parvoviridae) or "Bombyx mori" cypovirus 1 (BmCPV-1, Reoviridae). This either alone or in combination with bacterial infection destroys the gut tissue. Bacterial pathogens contributing to infectious flaccherie are "Serratia marcescens", and species of "Streptococcus" and "Staphylococcus" in the form known as thatte roga.

Louis Pasteur, who began his studies on silkworm diseases in 1865, was the first one able to recognize that mortality due to viral flacherie was caused by infection. (Priority, however, was claimed by Antoine Béchamp.) Richard Gordon described the discovery: "The French silk industry was meanwhile plummeting from a 130 million to an 8 million francs annual income, because the silkworms had all caught "pébrine," black pepper disease…He [Pasteur] went south from Paris to Alais, and rewarded them by discovering the silkworm epidemic to be inflicted by some sort of living microbe…Pasteur threw in another disease, "flâcherie," silkworm diarrhoea. The cures for both were culling the insects which showed the peppery spots — the peasants bottled the silkworm moths in brandy, for display to the experts — and rigorous hygiene of the mulberry leaf."

Specific types of enterocolitis include:

- necrotizing enterocolitis (most common in premature infants)

- pseudomembranous enterocolitis (also called "Pseudomembranous colitis")

Enteritis is inflammation of the small intestine. It is most commonly caused by food or drink contaminated with pathogenic microbes. but may have other causes such as NSAIDs, cocaine, radiation therapy as well as autoimmune conditions like Crohn's disease and coeliac disease. Symptoms include abdominal pain, cramping, diarrhoea, dehydration, and fever. Related diseases include inflammation of the stomach (gastritis) and large intestine (colitis).

Duodenitis, jejunitis and ileitis are subtypes of enteritis which are only localised to a specific part of the small intestine. Inflammation of both the stomach and small intestine is referred to as gastroenteritis. Inflammation of related organs of the gastrointestinal system are:

- gastritis

- gastroenteritis

- colitis

- enterocolitis

Infection is the invasion of an organism's body tissues by disease-causing agents, their multiplication, and the reaction of host tissues to the infectious agents and the toxins they produce. Infectious disease, also known as transmissible disease or communicable disease, is illness resulting from an infection.

Infections are caused by infectious agents including viruses, viroids, prions, bacteria, nematodes such as parasitic roundworms and pinworms, arthropods such as ticks, mites, fleas, and lice, fungi such as ringworm, and other macroparasites such as tapeworms and other helminths.

Hosts can fight infections using their immune system. Mammalian hosts react to infections with an innate response, often involving inflammation, followed by an adaptive response.

Specific medications used to treat infections include antibiotics, antivirals, antifungals, antiprotozoals, and antihelminthics. Infectious diseases resulted in 9.2 million deaths in 2013 (about 17% of all deaths). The branch of medicine that focuses on infections is referred to as infectious disease.

An opportunistic infection is an infection caused by pathogens (bacteria, viruses, fungi, or protozoa) that take advantage of an opportunity not normally available, such as a host with a weakened immune system, an altered microbiota (such as a disrupted gut flora), or breached integumentary barriers. Many of these pathogens do not cause disease in a healthy host that has a normal immune system. However, a compromised immune system, a penetrating injury, or a lack of competition from normal commensals presents an opportunity for the pathogen to infect.

An emerging infectious disease (EID) is an infectious disease whose incidence has increased in the past 20 years and could increase in the near future. Emerging infections account for at least 12% of all human pathogens. EIDs are caused by newly identified species or strains (e.g. Severe acute respiratory syndrome, HIV/AIDS) that may have evolved from a known infection (e.g. influenza) or spread to a new population (e.g. West Nile fever) or to an area undergoing ecologic transformation (e.g. Lyme disease), or be "reemerging" infections, like drug resistant tuberculosis. Nosocomial (hospital-acquired) infections, such as methicillin-resistant Staphylococcus aureus are emerging in hospitals, and extremely problematic in that they are resistant to many antibiotics. Of growing concern are adverse synergistic interactions between emerging diseases and other infectious and non-infectious conditions leading to the development of novel syndemics. Many emerging diseases are zoonotic - an animal reservoir incubates the organism, with only occasional transmission into human populations.

Secondary peritonitis and intra-abdominal abscesses including splenic and hepatic abscesses generally occur because of the entry of enteric micro-organisms into the peritoneal cavity through a defect in the wall of the intestine or other viscus as a result of obstruction, infarction or direct trauma. Perforated appendicitis, diverticulitis, inflammatory bowel disease with perforation and gastrointestinal surgery are often associated with polymicrobial infections caused by aerobic and anaerobic bacteria, where the number of isolates can average 12 (two-thirds are generally anaerobes). The most common aerobic and facultative bacteria are "Escherichia coli", "Streptococcus" spp. (including Enterococcus spp.), and the most frequently isolated anaerobic bacteria are the "B. fragilis" group, "Peptostreptococcus" spp., and "Clostridium" spp.

Abdominal infections are characteristically biphasic: an initial stages of generalized peritonitis associated with "Escherichia coli" sepsis, and a later stages, in which intra abdominal abscesses harboring anaerobic bacteria ( including "B. fragilis" group ) emerge.

The clinical manifestations of secondary peritonitis are a reflection of the underlying disease process. Fever, diffuse abdominal pain, nausea and vomiting are common. Physical examination generally show signs of peritoneal inflammation, isuch as rebound tenderness, abdominal wall rigidity and decrease in bowel sounds. These early findings may be followed by signs and symptoms of shock.

Biliary tract infection is usually caused by "E. coli, Klebsiella" and "Enterococcus" spp. Anaerobes (mostly "B. fragilis" group, and rarely "C. perfringens") can be recovered in complicated infections associated with carcinoma, recurrent infection, obstruction, bile tract surgery or manipulation.

Laboratory studies show elevated blood leukocyte count and predominance of polymorphonuclear forms. Radiographs studies may show free air in the peritoneal cavity, evidence of ileus or obstruction and obliteration of the psoas shadow. Diagnostic ultrasound, gallium and CT scanning may detect appendiceal or other intra-abdominal abscesses. Polymicrobial postoperative wound infections can occur.

Treatment of mixed aerobic and anaerobic abdominal infections requires the utilization of antimicrobials effective against both components of the infection as well as surgical correction and drainage of pus. Single and easily accessible abscesses can be drained percutaneously.

A contagious disease is a subset category of transmissible diseases, which are transmitted to other persons, either by physical contact with the person suffering the disease, or by casual contact with their secretions or objects touched by them or airborne route among other routes.

Non-contagious infections, by contrast, usually require a special mode of transmission between persons or hosts. These include need for intermediate vector species (mosquitoes that carry malaria) or by non-casual transfer of bodily fluid (such as transfusions, needle sharing or sexual contact).

The boundary between contagious and non-contagious infectious diseases is not perfectly drawn, as illustrated classically by tuberculosis, which is clearly transmissible from person to person, but was not classically considered a contagious disease. In the present day, most sexually transmitted diseases are considered contagious, but only some of them are subject to medical isolation.

Feline infectious anemia (FIA) is an infectious disease found in felines, causing anemia and other symptoms. The disease is caused by a variety of infectious agents, most commonly "Mycoplasma haemofelis" (which used to be called "Haemobartonella"). "Haemobartonella" and "Eperythrozoon" species were reclassified as mycoplasmas. Coinfection often occurs with other infectious agents, including: feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), "Ehrlichia" species, "Anaplasma phagocytophilum", and Candidatus "Mycoplasma haemominutum".

Caseous lymphadenitis (CLA) is an infectious disease caused by the bacterium "Corynebacterium pseudotuberculosis" found mostly in goats and sheep that at present has no cure. It manifests itself predominantly in the form of large, pus-filled cysts on the neck, sides and udders of goats and sheep. The disease is spread mostly from an animal coming in contact with pus from a burst cyst on an infected animal, but the disease is highly contagious and is thought to also be spread by coughing or even by flies. Studies have found CL incidence in commercial goat herds as high as 30%.