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Background: Human papillomavirus (HPV)‐associated subsequent malignant neoplasms (SMNHPV) in childhood cancer survivors are poorly understood. Methods: The cumulative risk of SMNHPV was assessed among 24,363 Childhood Cancer Survivor Study participants. Standardized incidence ratios (SIRs) and absolute excess risk were calculated using age‐matched, sex‐matched, and calendar year rates from the Surveillance, Epidemiology, and End Results program. Poisson regression models identified SMNHPV risk factors, evaluating relative SIRs (rSIR) and 95% confidence intervals (95% CIs). Results: In total, 46 survivors developed an SMNHPV (median age, 31 years [range, 10‐56 years]; median time from primary cancer, 21 years [range, 9‐35 years]). SMNHPV sites included oropharynx (N = 44), anorectum (N = 6), uterine cervix (N = 2), and vulva (N = 2). The 33‐year cumulative incidence was 0.3% (95% CI, 0.2%‐0.4%), and the SIR was nearly 3‐fold that of the general population (SIR, 2.86; 95% CI, 2.05‐4.00). Female survivors were not at increased risk of cervical or vulvar cancers compared with the general population. All survivors had an elevated risk of oropharyngeal SMNHPV (males: SIR, 4.06; 95% CI, 2.37‐6.97; females: SIR, 8.44; 95% CI 4.88‐14.61) and anorectal SMNHPV (males: SIR, 13.56; 95% CI, 5.09‐36.13; females: SIR, 9.15; 95% CI, 2.29‐36.61). Males (vs females: rSIR, 1.99; 95% CI, 1.00‐3.94); head, neck, and pelvic radiotherapy doses >3000 centigray (vs none: rSIR, 2.35; 95% CI, 1.11‐4.97); and cisplatin‐equivalent doses >400 mg/m2 (vs none: rSIR, 4.51; 95% CI, 1.78‐11.43) were associated with increased SMNHPV SIRs in multivariable analysis. Conclusions: Childhood cancer survivors are at increased risk for SMN in sites susceptible to HPV‐associated malignancies. Further research examining HPV in the etiology of SMN and the promotion of HPV vaccination and surveillance guidelines for SMNHPV in cancer survivors is warranted. Childhood cancer survivors are at increased risk for subsequent malignant neoplasms in anatomic sites associated with human papillomavirus infection. The promotion of prevention and surveillance strategies for these subsequent malignancies is warranted in this population. [ABSTRACT FROM AUTHOR]