Infection with high-risk HPV genotypes increases the risk for persistent or progressive cervical lesions. The aim of this study was to determine the frequency and correlation of the HPV infection with the cytological or histopathological diagnosis. A total of 6988 samples were analysed and after exclusion of the repeated samples and/or those containing degraded DNA, 4421 patients were included in the study group. PCR-RFLP technique was used as a method for HPV typing. HPV infection was detected in 1819 out of 4421 patients. The frequency of infection was 23% in the patients’ group with cytological and 60% in the group with histopathological diagnosis. The HPV frequencies in precursor lesions were as follows: 51% in patients with mild; 75% in patients with moderate; 91% in patients with severe dysplasia and 93% in carcinoma in situ lesions. The most prevalent HPV types in descending order were: HPV 16, 31, 53, etc. HPV infection was the most frequent in patients under 19 years old. In 169 out of 1253 samples with determined viral genotype, a multiple infections were found. This data for the prevalence and distribution of the HPV infection in Macedonian women accentuates the need for the establishment of organized screening programs.