Abstract： AIM:To explore the reasons of human papillomavirus (HPV)in esophageal cancer detected vary. METHODS:HPV16-DNA detected by polymerase chain reaction(PCR)in 30 the same surgical resection of esophageal cancer specimens in frozen and paraffin embedded matched. RESULTS:Detection rates of HPV involved in 30 frozen esophageal cancer specimens was 84% ,53% in corresponding to paraffin fixed tissue, respectively. Three frozen specimens with HPV-negative in their paraffin counterparts were negative, twenty-seven cases frozen tissue samples with only 16 cases in paraffin detected HPV16-DNA in existence.CONCLUSION:For the highly divergent detection rates of HPV in esophageal carcinoma, in addition to different geographical factor, by the application of different detection methods, it should be attributed to materials processed in different methods, and caused a lot of small DNA fragmentation, even beyond the scope to be amplified.