Background: We analysed the temporal relationships of the clearance of human papillomavirus (HPV) DNA and cytological abnormalities in women participating in a screening study in three NIS countries. Methods: The 274 patients included in this analysis were prospectively followed-up for 21.6 months (range: 0.5–42.9). All 274 women had abnormal PAP test (ASC-US or higher) and high-risk HPV-positive test (HCII) at baseline. Two groups were compared: 132 women who cleared both tests (Group 1), and 142 women who cleared either HPV or abnormal PAP test (Group 2). The first clearance during the follow-up, and the last visit clearance were modeled using life-table techniques, and the predictive factors were analysed using univariate (Kaplan–Meier) and multivariate (Cox) survival analysis. Results: There was no difference in the mean clearance time for the abnormal PAP test (14.4 months; 0.7–40.5 and 12.6 months; 0.5–35.0) and high-risk HPV DNA (12.67 months; 0.6–33.5 and 10.8 months; 0.7–33.4) in Group 1 and Group 2 (Mann–Whitney: P = 0.107 and P = 0.082, respectively). Clearance times for HPV DNA and abnormal PAP test did not deviate from each other in either groups (Wilcoxon: P = 0.063 and P = 0.088). The monthly clearance rates for the abnormal PAP test are 1.32 and 1.38%, and those for the HPV DNA 1.62 and 1.61%, in Groups 1 and 2, respectively. Of the factors predicting the last visit clearance, the issues related to smoking are of particular interest. Conclusions: The clearance of high-risk HPV type and abnormal PAP test shows a close temporal relationship, the former preceding the latter, however, by an interval of 1.0–2.0 months.