Ten patients with the acquired immunodeficiency syndrome and an endoscopic erosive/ulcerative lesion in esophagus (4), stomach (3), or colon (3) were prospectively studied with multiple biopsies (244 biopsies from 33 sites) to determine: 1) the frequency of positive tests for cytomegalovirus (CMV) in the lesions versus normal mucosa, 2) the influence of number of biopsies on the rate of positivity. As seen on histology, five out of 10 lesions had cytomegalic cells, but only six of 45 (13%) of the biopsies taken from lesions that were positive showed the diagnostic changes. Immunoperoxidase was positive in two of the lesions with cytomegalic cells, but the positive staining occurred in only three of 35 (9%) biopsies from the histologically positive lesions. Culture was positive in one of 10 lesions, and the rate of positivity did not depend on number of cultures sent or number of biopsies per culture. Polymerase chain reaction was positive in six of 10 lesions, including all lesions positive by either histology (5), immunoperoxidase stain (2), or culture (1). The frequency of a biopsy being positive for CMV in normal mucosa was found to be 4%, 0%, 17%, and 28% by histology, immunoperoxidase stain, culture, and polymerase chain reaction, respectively. In AIDS patients at high risk for CMV, histologic evidence of CMV infection is uncommon in normal mucosa but is frequent in suspicious lesions. However, the frequency of diagnostic histology is highly dependent on the number of biopsies taken and the diligence of the pathologist. Polymerase chain reaction has the potential to become a rapid test to rule out CMV infection in gastrointestinal tissue.