Identifying the etiology of hepatic dysfunction in liver transplant patients is critical to their clinical management and in maintaining graft survival. While cytomegalovirus (CMV) is a well-known cause of posttransplant hepatitis, the morphologic diagnosis of CMV hepatitis in liver biopsies can be difficult. Because conventional tissue culture for CMV requires days to weeks, the final results often arrive too late to be clinically useful. In this study, 44 liver allograft biopsies from 21 patients with hepatic dysfunction were evaluated for CMV by routine light microscopy, conventional tissue culture, and in situ DNA hybridization (IH) using commercially available biotinylated CMV-specific DNA probes. Whereas 38.6% of the biopsy specimens were positive by IH, 15.9% were culture-positive biopsies and 13.6% were positive by routine light microscopy. Assuming tissue culture to be the standard, IH demonstrated a sensitivity of 100% and a specificity of 73%. In comparison, routine light microscopy showed a sensitivity of 71.4% and specificity of 97.3%. In addition, three biopsy specimens positive only by IH were from three patients who had other liver biopsies positive for CMV by either light microscopy or viral culture. In situ DNA hybridization allows rapid detection (5-6 h) of CMV in paraffin-embedded liver allograft biopsies; it also has a sensitivity that surpasses routine histologic examination and perhaps even tissue culture.