Condyloma acuminatum (CA) has high recurrence rates after local treatments. Why this lesion is difficult to eradicate is unclear. One possible explanation for recurrence after superficial destructive therapy is the presence of residual human papillomavirus (HPV) in the superficial dermis beneath the treated epidermis. Thirteen samples of CA were excised from 13 patients. Thirteen samples of basal cell carcinoma (BCC) were studied for purposes of control. Epidermis was separated from dermis by treatment with sodium bromide. DNA was extracted from both tissues and used sodium bromide solution and amplified for the presence of HPV DNA using the polymerase chain reaction. HPV DNA was detected in the epidermis of 11 samples of CA. HPV type 6 was seen in 7 specimens; HPV type 11, in 4. HPV DNA was found in the dermis of 3 specimens of CA; type 6 in 2 and type 11 in 1. Two samples were excluded because of contamination of the sodium bromide solution by HPV. HPV DNA was not detected in tissue samples from BCC. The presence of HPV DNA in the dermis of some condylomata may explain recurrence in sporadic cases.