AbstractIn situ hybridization is a commonly used technique for the detection of nucleic acid sequences but its efficacy can be affected by many parameters. Human papillomavirus (HPV) infection of the genital tract is a useful model for determining how the various parameters may effect the hybridization signal. In this study, the rate of detection of HPV DNA was compared for 294 genital tract lesions fixed in Bouin solution and 306 lesions fixed in buffered formalin. The detection rate in low grade vulvar and cervical intraepithelial lesions fixed in buffered formalin was 96% and 91%, which compared to 83% and 76% , respectively, of tissues fixed in Bouin solution. The detection rate was 73% and 70% for vulvar and cervical high grade intraepithelial lesions fixed in buffered formalin, respectively, versus 50% and 47% for the comparable tissues fixed in Bouin solution. Thus, the decrease in the detection rate was greater for both the vulvar and cervical high grade lesions compared to the low grade lesions for tissues fixed in Bouin solution (33% and 29%) than for tissues fixed in buffered formalin (23% and 21%). This relative greater decrease in the detection rate for Bouin fixed tissues reflects the lower copy number found in high grade lesions relative to low grade lesions. These findings demonstrate that both the fixative and the histologic findings impact on the in situ hybridization results for HPV related lesions. (The J Histotechnol14:13, 1991)