Abstract Background: It is largely unknown if antihuman papillomavirus (HPV) serum antibody responses vary by anatomic site of infection in men. Methods: This study assessed type-specific anti-HPV serum antibody prevalence associated with corresponding HPV DNA detection in the external genitalia and the anal canal of 1,587 heterosexual men and 199 men who have sex with men (MSM). Results: We observed that HPV 6 and 16 seroprevalence was higher in the presence of same HPV-type infection in the anal canal compared with same HPV-type infection in the external genitalia only, and among MSM compared with the heterosexual men. Seropositivity to HPV 6 was strongly associated with HPV 6 DNA detection in the anal canal but not in the external genitalia alone among both heterosexual men [adjusted prevalence ratio (APR), anal+/genital+ vs. anal−/genital−: 4.2, 95% confidence interval (CI), 11.7–10.5; anal+/genital− vs. anal−/genital−: 7.9 (95% CI, 3.7–17.0)] and MSM [APR, anal+/genital+ vs. anal−/genital−: 5.6 (95% CI, 2.7–11.9); anal+/genital− vs. anal−/genital−: 3.2 (95% CI, 2.1–4.9)]. Similar associations between seropositivity to HPV 16 and anal HPV 16 DNA detection were only observed in MSM [anal+/genital+ vs. anal−/genital−: 3.1 (95% CI, 2.0–5.0); anal+/genital− vs. anal−/genital−: 2.2 (95% CI, 1.3–3.5)]. Conclusion: Our data showed that seroprevalence varied by anatomic site of HPV infection, suggesting differences in epithelium type present at these anatomic sites may be relevant. Impact: Our finding is instrumental in advancing our understanding of immune mechanism involved in anatomic site–specific antibody response. Cancer Epidemiol Biomarkers Prev; 21(9); 1542–6. ©2012 AACR.