The prevalence of human papillomavirus (HPV) infection and other risk factors were studied in a high risk area for cervical cancer (Greenland) and in a low risk area (Denmark). From Nuuk (Greenland) and Nykøbing Falster (Denmark), random samples of 150 women aged 20-39 years were drawn. A total of 129 and 126 women were included in Greenland and Denmark, respectively. The proportion of HPV infected women assessed by ViraPap was similar in Denmark and Greenland (4.8 vs 3.9%). When type specific polymerase chain reaction (PCR) was used, the total HPV detection rate was 38.9% in the Danish population and 43.4% in the Greenlandic. A similar interrelationship between Greenland and Denmark applied to the HPV types 11, 16, 18 and 33. No relationship was observed between HPV detection and number of partners for any of the diagnostic methods. Significantly more Greenlandic than Danish women had antibodies to HSV 2, 76.0% and 26.2%, respectively. The prevalence of self-reported histories of selected venereal diseases was also highest among Greenlanders, except for genital warts where the prevalence was similar in the two areas. Greenlandic women had significantly more sexual partners, earlier age at first intercourse, more current smokers and less use of barrier contraceptives compared to the Danish women. This study confirms the results of our previous population-based cross-sectional comparison study in these areas, corroborating the conclusion that the prevalence of detectable HPV infection does not seem to be a determinant of cervical cancer incidence. However, by using DNA hybridisation techniques, temporal virus shedding is only measured at one point in time. Detectable virus shedding may not correlate with the risk of cervical cancer. In fact, HPV DNA detection may have different implications in different populations. In Denmark, HPV DNA detection may reflect transient, recently acquired infection, whereas in Greenland, it is more indicative of chronic persistent infection.