High‐ and low‐grade cervical lesions were analyzed for the presence of polyomavirus (PYV) and human papillomavirus (HPV) sequences. In precancerous cervical lesions, the overall prevalence of PYV sequences was 44% (41/93). Specifically, among the PYV‐positive samples, 83% (34/41) tested positive for BK polyomavirus (BKV) sequences, whereas 17% (7/41) were positive for JC‐virus. None of the samples were positive for simian virus 40. The presence of BKV DNA in high‐grade squamous intraepithelial lesions was confirmed by in situ PCR. BKV sequences were detected more frequently in high‐grade squamous intraepithelial lesions, together with the genotype HPV‐16. The association of BKV with precancerous cervical lesions suggests that this polyomavirus participates with HPV‐16 in the cell transformation process. Alternatively, BKV might multiply better in HPV‐16‐positive cells from precancerous cervical lesions than in HPV‐16‐negative cells. J. Med. Virol. 83:1770–1776, 2011. © 2011 Wiley‐Liss, Inc.