Gastrointestinal (GI) disorders, mainly diarrhea, are a defining feature of human immunodeficiency virus (HIV) infection. Persistent diarrhea in the absence of infectious pathogens other than HIV itself is classified as HIV enteropathy. Thus, HIV enteropathy is defined and also identified in HIV-infected patients by excluding other organisms as the cause of persistent diarrhea.
HIV infection presents in the majority of cases with diarrhea and associated complaints, which are either due to opportunistic organisms or HIV itself. The introduction of highly active antiretroviral therapy (HAART) has had a striking effect on all aspects of HIV infections, among which has been a decline in intestinal colonization by opportunistic pathogens. Nevertheless, such infections still occur and cause diarrhea.
Intestinal pathogen-negative HIV enteropathy also persists in spite of HAART. The presentation, in addition to diarrhea, the most common symptom, includes a variety of features such as dysphagia, nausea, and abdominal pain. The anomalies observed in the GI tract in HIV enteropathy, such as inflammation, elevated permeability, malabsorption of some substances, villous atrophy and crypt hyperplasia account for the symptoms. HIV may be responsible for some of the GI pathologies was suggested early on by the observation that the virus could directly infect gastrointestinal cells in the crypts and lamina propria .
A variety of mechanisms have been suggested to account for the direct and indirect effects of the HIV virus on intestinal physiology:
Careful recording of the patient’s history will reveal whether diarrhea perceived by the patient is indeed present according to clinical standards  and whether it may be due to food allergies, or medications. Among the medications are components of the HAART regimens, which in themselves may be the cause of GI symptoms. Some of the protease inhibitors are especially problematic in this respect  .
Symptoms accompanying the diarrhea are helpful in localizing the affected segment of the GI tract: cramps and bloating indicate the small bowel, whereas hematochezia and tenesmus suggest the involvement of the large bowel. The two sections of the GI tract are colonized by different opportunistic organisms. Some of the organisms in the upper tracts (small bowel) are protozoa and fungi (cryptosporidia, cyclosporidia, and microsporidia), while some of those in the colon are bacteria and viruses (such as campylobacter, clostridium difficile and cytomegalovirus). CD4 cell counts should be determined to assess the competence of the immune system: opportunistic infections do not usually occur if the immune system is not too compromised (CD4 counts greater 200 cells/microliter) .
Culturing of the stool and its examination in the microscope for cysts, ova, and parasites are early diagnostic tests mandatory for deciding whether or not the diarrhea is due to opportunistic organisms.  The polymerase chain reaction and immune assays are also used to identify some of the organisms. If the stool samples do not contain identifiable organisms, and if diarrhea seriously impacts the quality of life, invasive methods, such as endoscopy, sigmoidoscopy, or colonoscopy are used to isolate opportunistic organisms and to examine the GI tract. In several studies, colonoscopy and endoscopy together with tissue biopsy identified opportunistic pathogens in about a quarter to half of the patients whose stool samples were pathogen free .
If none of these methods show opportunistic pathogens, the diagnosis of HIV enteropathy can be made, bearing in mind that with advances in technology new pathogens are being discovered, such as atypical viruses .
In general, the diagnostic effort should concentrate on finding treatable conditions to lessen the detrimental effect of diarrhea on the quality of life .