Although the lineages of human papillomavirus type 31 (HPV31) variants are recognized, their clinical relevance is unknown. The purpose of our study was to examine risk of cervical intraepithelial neoplasia Grades 2-3 (CIN2/3) by HPV31 variants. Study subjects were women who participated in the atypical squamous cells of undetermined significance and low-grade squamous intraepithelial lesion Triage Study and who had HPV31 infections detected at one or more visits. They were followed semi-annually over 2 years for detection of HPV DNA and cervical lesion. HPV31 isolates were characterized by DNA sequencing and assigned into 1 of 3 variant lineages. CIN2/3 was histologically confirmed in 127 (27.0%) of the 470 HPV31-positive women, 83 diagnosed at the first HPV31-positive visit and 44 thereafter. The odds ratio for the association of 2-year cumulative risk of CIN2/3 was 1.7 (95% CI: 1.0-2.9) for infections with A variants and 2.2 (95% CI: 1.2-3.9) for infections with B variants as compared to those with C variants. Among women without CIN2/3 at the first HPV31-positive visit, the risk of subsequent CIN2/3 was 2.2-fold greater for those with A variants (95% CI: 1.0-4.8) and 2.0-fold greater for those with B variants (95% CI: 0.9-4.9) as compared to those with C variants. Similar associations were observed when CIN3 was used as the endpoint. The findings from our study help to tag HPV31 variants that differ in risk of CIN2/3 and to explain in part why some HPV31 infections regress spontaneously and others lead to disease progression.Cervical infection with human papillomavirus (HPV) types is a necessary cause of cervical cancer and its precursor, cervical intraepithelial neoplasia Grades 2-3 (CIN2/3). 1-3 To date, >150 papillomavirus types have been fully characterized and classified, from the higher to lower taxon, as genera, species and type. 4,5 HPV types are known to differ in their tropisms and oncogenic potentials. Studies of the intratypic variation, i.e., the variant, a level below the taxon of type, have focused mainly on HPV16 and HPV18, showing that some variants were more aggressive than others. [6][7][8][9][10][11][12] HPV31 is one of the oncogenic types, most closely related to HPV16. Prevalence of some HPV types may vary geographically. Results from a recent meta-analysis (including 215 studies worldwide) have shown that on average prevalence of HPV31 infection ranks fourth, after types 16, 18 and 45, in cases of cervical cancer and second, only after type 16, in women with high-grade squamous intraepithelial lesion (referring both to cytologically detected high-grade lesions and histologically diagnosed CIN2/3 or carcinoma in situ in this analysis). 1 Clinical relevance of HPV31 variants has been rarely described, 13-15 although the intratypic variations in the L1, E6, E7 and long control region were recognized. 14-21 A recent study by Chen et al. 22 has defined HPV31 variants as A, B and C lineages based on the whole genome analyses. This provides a basis to view the variant as a distinct phylogenet...