BACKGROUND To determine the relationship between human papillomavirus infection, cervical carcinoma, pre-cancerous lesion and condyloma acuminatum. METHODS From January 2004 to August 2005, 1086 inpatients in department of dermatology and department of gynaecology and obstetrics in Southwest Hospital and No. 302 Hospital with cervical lesions and condyloma were reviewed. All specimens were detected for HPV-DNA using techniques of Gene Array and fluorogenic quantitative polymerase chain reaction (FQ-PCR). All detections of HPV-DNA were performed in the first admission before the patients underwent any examination or treatment. RESULTS The positive rates of HPV-DNA detection were 100% in cervical intraepithelial neoplasia (CIN) I, and II and cervical carcinoma. Among these, the main subtype was HPV 16. But some of the patients were found to be positive for more than 2 subtypes of HPV. While the commonest HPV subtype was HPV 18 in endometrial cancer. Some of the patients were detected to be positive for more than 2 subtypes of HPV. In 636 female patient with condyloma acuminatum, the infection rates of HPV6, HPV11 accounted for 44.97% and 29.40%, respectively, HPV 16 and/or HPV 18 infection constituted a small percentage. In a few cases, infection with more than 2 subtypes was detected. CONCLUSION Cervical carcinoma including pre-cancerous lesion differs from condyloma acuminatum in dominate infectious subtype of HPV. The former is mainly associated with HPV 16 and HPV 18 infections, and the latter mainly associated with HPV 6 and HPV 11 infections. But in both of the above lesions, a mixed infection with more than 2 types may occur and make the pathological changes and clinical treatment more complicated. The early diagnosis and supervision of HPV infection may be of great value for improvement of prognosis and quality of life.