Objectives. Infection with high-risk human papillomavirus (HPV) is a critical factor associated withcarcinogenesis of the uterine cervix. HPV-16 is most frequently found, and is further subclassified into intratypicvariants based on the nucleotide sequences of the viral genes. Although certain HPV-16 variants are reported tobe associated with the progression of cervical lesions, these relationships remain controversial with differentresults for different populations. To provide data for another population, we investigated the prevalence ofHPV-16 and distributions of its intratypic variants among Mongolian women with cervical intraepithelialneoplasia (CIN) and invasive cervical cancer. Materials and Methods. We analyzed samples from 374 randomlyselected women who attended the National Cancer Center of Mongolia between January 2002 and July 2007,including 147 invasive cervical cancer patients, 127 CIN patients and 100 age-matched controls who werecytologically normal. HPV genotyping was initially conducted, followed by variant analysis for HPV-16-positivesamples by nucleotide sequencing of the E6 gene. The HPV data were evaluated statistically for correlationswith the patients’ clinical data. Results. HPV genotyping detected 101 HPV-16-positive samples. Among thesesamples, 92 were available for subsequent variant analysis, including 66 invasive cervical cancer samples, 25CIN samples and 1 cytologically normal sample. A total of 14 different variants were identified. All 14 variantsbelonged to the European lineage, and the European prototype was detected in 66% (61/92) of the samples.Among the remaining 31 variants, variants with the T350G nucleotide change were predominant (13/31, 42%),followed by variants containing G94A (11/31, 35%), G176A (4/31, 13%) and G274T (2/31, 7%) . There were nosignificant differences among all the variants regarding their distributions in CIN and invasive cervical cancers.Conclusions. HPV-16 variants of the European lineage were exclusively distributed among the Mongolian womenexamined, and the European prototype was overwhelmingly predominant. Since no significant differences werefound between the types of variants and severities of the cervical lesions, it is possible that racial or geographicfactors may have some influences on these relationships.