Objectives: This study aims to identify the differences in the use of HPV vaccination between female medical students in the Czech and Slovak Republics and their possible causes. Methods: We performed a cross-sectional survey among female students of general medicine in all faculties of medicine in the Czech and Slovak Republics. Results: We obtained 630 questionnaires from the Czech Republic and 776 questionnaires from the Slovak Republic. In the Czech Republic, 65.4% of female medical students underwent HPV vaccination, while in the Slovak Republic, the figure was 21.1%. In the Czech Republic, residency and religion of students did not influence their rate of vaccination. However, in the Slovak Republic, village residency with less than 5,000 inhabitants lowered the probability of vaccination with OR = 0.56 (95% CI: 0.38-0.84), and the Catholic religion lowered the probability of vaccination with OR = 0.40 (95% CI: 0.28-0.57). Czech students were informed about the possibility of vaccination by a paediatrician in 55.7% of cases, while the figure for Slovak students was 26.8%. In the Czech Republic, 75.7% of students participated in regular cervical oncologic screening, while in the Slovak Republic, the figure was 57.7%. Vaccination of relatives would be recommended by 86.5% and 80.5% of Czech and Slovak students, respectively. Conclusions: The adoption of an oncologic prevention programme and the more extensive propagation by paediatricians are probably the medical reasons for the higher HPV vaccination among Czech students. Demographic factors - village residency and religion - are also important.