The Human Papilloma Virus (HPV) has significant importance in invasive cervical cancer etiology of and its precursory injuries. Thus, it is necessary the application of molecular methodologies for the precocious diagnosis of this infection. This research has evaluated the effectiveness of Hybrid Capture System (HCS) in detecting pathogenic types of HPV. HCS was compared with empirical established cytological criteria in specimens with cellular alterations that were suggestive of HPV infection. The presence of HPV was also evaluated in cytological normal specimens with inflammation and Cervical Intraepithelial Neoplasia (CIN). One hundred and eight women, suspected of HPV infection (clinical or cytological suspicion), were selected. Results demonstrated that both methods were complementary, since Hybrid Capture confirmed results of the cytology. The two methods may be used together to improve the diagnosis. Furthermore, the use of Hybrid Capture test in HPV diagnosis allows the identification of the risk that the virus proportionate.