The anatomical and immunological parallels between cervical and anal canals raise questions about shared HPV pathogenesis. This study evaluated the concordance of HPV/cytology between sites and their association with histopathology. We retrospectively analyzed 984 women who underwent concurrent cervical/anal cytology and HPV testing (Jan, 2019–Jun, 2024). Subgroups included 706 with colposcopy‐histopatholgoy and 265 with HRA‐histopathology. Consistency was assessed using chi square tests, Cramér's V, and diagnostic performance metrics. HPV‐16 dominated both sites (cervix: 27.54%; anus: 21.44%). Cervical‐anal cytology showed weak‐moderate agreement (Cramér's V = 0.225, p < 0.001), while HPV genotyping demonstrated stronger concordance (V = 0.458, p < 0.001), especially for HPV‐16/18 (60%, 180 anal positive in 300 cervical positive). Histopathology correlation was weak (Spearman's ρ = 0.261). Anal HPV predicted anal LSIL+ poorly (PPV = 43.7%, AUC = 0.55). Combined anal HPV/LCT screening improved sensitivity (89.2%) but reduced specificity (22.1%). While cervical and anal HPV infections are moderately associated, the considerable site‐specific disparities in cytological and histopathological findings underscore the need for independent clinical assessment of each site.