HIV positive or otherwise immunosuppressed patients are susceptible to cervicovaginal infections with a wide spectrum of HPV types. The aim of our study was to investigate the distribution of HPV in squamous intraepithelial lesions (SIL) with regard to HIV infection. We evaluated the HPV status in 20 HIV positive women with cytologically assessed SIL (11 high grade, 9 low grade) in relation to clinical and histological/cytological findings. Twenty HIV negative patients (15 high grade, 5 low grade SIL) served as a control. HPV typing was performed by polymerase chain reaction followed by PCR-ELISA (HPV 6/11, 16/18, 31/33, 40, 45, 52, 58) or sequence analysis of the amplicon (HPV 73, 87). HPV 52 was the most common type in the HIV positive group (8 HIV positive cases vs. 1 HIV negative case). HPV 16/18 was found in 6 HIV positive and 11 HIV negative patients. Further types detected in HIV positive patients were HPV 40, 58, 73 and 87 (one case each). No correlation was found between the HPV status and the CD4+ count or the grading of SIL. Persisting HPV infection with recurrence of SIL was documented in 5 cases after initial therapy of HPV positive lesions (HPV 87, 73, 58, 31/33, 16/18). HIV infected patients reveal a wider spectrum of HPV types in cervicovaginal SIL than HIV negative women. Especially HPV 87 and its relation with HIV infection and development and persistence of SIL needs further investigation. Our results indicate the inclusion of otherwise rare HPV types in screening programs for HIV positive and immunosuppressed patients.