BACKGROUND: Youth with perinatally acquired HIV (YPHIV) are at higher risk of anogenital human papillomavirus (HPV) infection. METHODS: We enrolled a cohort of YPHIV and HIV-negative youth in Thailand and Vietnam, matched by age and lifetime sex partners, and followed them over 144 weeks (to 2017). Participants had annual pelvic examinations with samples taken for HPV genotyping. Concordant infection was simultaneous HPV detection in multiple anogenital compartments (cervical, vaginal, anal); sequential infection was when the same type was found in successive compartments (cervico-vaginal to/from anal). Generalized estimating equations were used to assess factors associated with concordant infection, and Cox regression to assess factors associated with sequential infection. RESULTS: A total of 93 YPHIV and 99 HIV-negative females were enrolled; median age 19 (IQR 18-20) years. High-risk anogenital HPV infection was ever detected in 76 (82%) YPHIV and 66 (67%) HIV-negative youth over follow-up. Concordant anogenital high-risk HPV infection was found in 62 (66%) YPHIV vs. 44 (34%) HIV-negative youth. Sequential cervico-vaginal to anal high-risk HPV infection occurred in 20 YPHIV vs. 5 HIV-negative youth; incidence rate 9.76 (6.30-15.13) vs. 2.24 (0.93-5.38) per 100 person-years. Anal to cervico-vaginal infection occurred in 4 YPHIV vs. 0 HIV-negative females; incidence rate 1.78 (0.67-4.75) per 100 person-years. Perinatally acquired HIV was the one factor independently associated with both concordant and sequential high-risk HPV infection. CONCLUSIONS: Children and adolescents with perinatally acquired HIV should be prioritized for HPV vaccination, and cervical cancer screening should be part of routine HIV care for sexually active YPHIV.