Recent reports have suggested that routine microscopic evaluation of anal ulcer tissue from AIDS patients is not the most accurate way to diagnose viral infection. This study was undertaken to determine if either viral culture (VC) or immunohistochemistry (IHC) can improve the diagnostic accuracy as compared with routine hematoxylin and eosin (H&E) staining. Specifically, we sought to identify inclusion bodies of cytomegalovirus (CMV) or herpes simplex virus (HSV) to assist in the diagnosis of CMV or HSV. All patients had clinical evidence of an anal ulcer or a nonhealing anal fissure. Duration of symptoms ranged from 1 week to 3 months with a mean of 6 weeks. All specimens were submitted for viral culture in addition to routine H&E staining; immunohistochemistry was also performed. Twenty-five paraffin-embedded anal ulcer biopsies from 23 male patients (age range 27-73; mean 37.4 years) with the diagnosis of AIDS or AIDS-related complex (ARC) were reviewed over a 4 year period (1988-1992). Routine H&E staining revealed 6 (22%) specimens with CMV inclusions. Four of these 6 reacted positively with IHC (67%) and one was positive on viral culture (17%). In the remaining 19 specimens that did not reveal infection with CMV (78%), IHC was positive in 2 patients (10%) and viral culture was positive in 1 patient (5%). Although HSV was not seen in any of the specimens on H&E staining, IHC was positive in one patient (3.5%) and viral culture reacted positively in 8 (29%) specimens. Thus IHC is a good confirmatory test for CMV inclusions and can be used to achieve a definitive diagnosis in equivocal cases.(ABSTRACT TRUNCATED AT 250 WORDS)