This study determined the prevalence, cellular localization, and content of human immunodeficiency virus (HIV)-associated antigens in intestinal mucosa from HIV-infected subjects. Studies were performed in 168 subjects with gastrointestinal, nutritional, or proctologic complaints, and HIV-seronegative controls. The polymerase chain-reaction technique, which detects viral DNA, was used in 20 subjects and was positive in 70%. In situ hybridization studies, using RNA probes, were employed in 48 cases and were positive in 31%. Immunohistologic studies using monoclonal antibodies to HIV p24 antigen were employed in 73 cases and were positive in 67%. Quantitative ELISA assays for tissue p24 content were performed in 168 cases and was positive in 68%. Evidence of HIV was found throughout the intestine and in different disease stages. The quantitative ELISA studies correlated significantly with in situ hybridization, implying a possible association between the presence of viral RNA and protein expression. The authors conclude that HIV is present in intestinal mucosa from most, if not all HIV-infected subjects. The relationship to intestinal disease currently is unclear.