The age standardized death rate from cervical cancer in Aboriginal women in the Northern Territory (NT) for the period 1987 to 1993 was 11.5 times higher than the Australian average for the same period. This is the first study to determine HPV genotypes in both Aboriginal and non-Aboriginal women living in the Top End of the NT using a self-administered tampon technique for specimen collection. Women who attended sexually transmitted disease clinics and Family Planning Clinics in urban areas and community health centers in remote areas were asked to insert and immediately remove a tampon which was then tested for the presence of HPV genotypes using the polymerase chain reaction. A total of 646 female subjects were enrolled in the study. Subjects with HPV had a mean age of 26.1 years (SD 8.5), while those without HPV had a mean age of 29.8 years (SD 9.8) (P < 0.001). The oncogenic genotypes (16,18,31,33,35,39,45,51,52) accounted for 54.7%, while 23.1% of HPVs were untypable. The virus was detected in 161/287 (56.1%) of non-Aboriginal women and in 150/359 (41.8%) of Aboriginal women (P < 0.001). More than one genotype was detected in 40 subjects (12.8%); of these seven had three or more genotypes present. This study is the first to document the HPV genotypes occurring in females in the Northern Territory and shows that HPV is a common infection in both the Aboriginal and non-Aboriginal population.