Genital infection with high-risk human papillomavirus (HR HPV) associates with increased risk of developing precancerous lesions, such as cervical intraepithelial neoplasia (CIN). The objective of this pilot study conducted in north-east Croatia was to determine the prevalence of HPV genital infection in women with abnormal cervical cytology and to determine its association with their age and HPV genotype(s). From March 2009 to December 2011, cervical swabs from 100 women were analysed for HR HPV infection (AMPLICOR HPV Test, Roche Diagnostics) and genotyped for high risk (HR), intermediate (IR) and low risk (LR) HPVs (Linear Array HPV Genotyping Test, Roche Diagnostics). The most prevalent HR genotypes in women with CIN were HPV 16 (27.6%), HPV 31 (11.8%), HPV 51 and HPV 52 (10.2% each). The most prevalent IR genotypes were HPV 66 (30%) and HPV 62 (23.3%). The most prevalent LR genotype was HPV 6 (20.3%). Women between 21 and 25 years of age showed the highest rate of HPV infection (44.2%). Moreover, women younger than 35 years showed a significant association (p < 0.01) and positive correlation (r = 0.67; p < 0.05) between HR HPV infection and CIN stages 1 and 2. Multiple HPV infections were found in almost half of the women. This is the first study that analysed the prevalence of genital infection with HR/IR/LR HPVs in women with CIN from north-east Croatia. Despite the preliminary nature of this pilot study, the lower prevalence of some HR HPVs (HPV18) and the higher prevalence of other HR HPVs (HPVs 51, 52 and 31) may imply the necessity for the development of more targeted anti-HPV vaccines or other strategies for more efficient protection against oncogenic HPV infection in women from our region.