Human papillomavirus (HPV) infection is the most frequent sexually transmitted disease. According to current estimates, there are about 5 500 000 new infections diagnosed annually. Among about 100 known types of HPV, 40 are designed as genital due to their preferential affinity to vulvar, vaginal, cervical, penile and anogenital epithelium. Chronic infection with types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58 and 59 is associated with an elevated risk of malignant transformation, whereby the type 16 is detected in 50-55% of cases of invasive cervical cancer. Certain diagnosis of HPV infection at every stage of viral life cycle is provided by molecular virological techniques, while detection of viral DNA gains a novel significance as an adjunct to cytological study. Promising diagnostic potential in the setting of chronic HPV infections is associated with the test based on analysis of mRNA transcripts, enabling detection of active oncogenes E6 and E7 of the virus. This enables not only to confirm the presence of virus as such, but also to determine its activity gauged by initiation of transcription, i.e. the earliest phase of carcinogenesis. This is most useful the management of women infected by non-highly oncogenic HPV types. Most vulvar, vaginal and anal cancers are associated with HPV infection. Recently, the incidence of anogenital malignancies is increasing significantly. In view of continuously increasing number of HPV infections, it is reasonable to expect an increased number of anogenital malignancies and precursor lesions thereof, being diagnosed in the near future. Therefore, current epidemiological studied focus on inclusion of HPV testing (HPV DNA, HPV mRNA and early HPV genes) into large-scale screening programs for cervical cancer.