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The aim of the study was to estimate the magnitude of the association between HPV-related gynecological neoplasms and secondary anal cancer among women in Puerto Rico (PR).We identified 9,489 women who had been diagnosed with a primary cervical, vaginal, or vulvar tumor during 1987–2013. To describe the trends of invasive cervical, vulvar, vaginal, and anal cancer, the age-adjusted incidence rates were estimated using the direct method (2000 US as Standard Population). Standardized incidence ratios (observed/expected) were computed using the indirect method; expected cases were calculated using 2 methods based on age-specific rates of anal cancer in PR. The ratio of standardized incidence ratios of anal cancer was estimated using the Poisson regression model to estimate the magnitude of the association between HPV-gynecologic neoplasms and secondary anal cancer.A significant increase in the incidence trend for anal cancer was observed from 1987 to 2013 (annual percent change = 1.1, p < .05), whereas from 2004 to 2013, an increase was observed for cervical cancer incidence (annual percent change = 3.3, p < .05). The risk of secondary anal cancer among women with HPV-related gynecological cancers was approximately 3 times this risk among women with non–HPV-related gynecological cancers (relative risk = 3.27, 95% CI = 1.37 to 7.79).Anal cancer is increasing among women in PR. Women with gynecological HPV-related tumors are at higher risk of secondary anal cancer as compared with women from the general population and with those with non–HPV-related gynecological cancers. Appropriate anal cancer screening guidelines for high-risk populations are needed, including women with HPV-related gynecological malignancies and potentially other cancer survivors.