Oral human papilloma virus (HPV) infection is associated with nearly three-quarters of all oropharyngeal cancers in the United States. Research also suggests its association with periodontal disease. There are limited studies evaluating differences in HPV detection methods; however, oral rinse is considered the most sensitive detection method. We compared HPV detection by self-collected oral rinse versus self-collected cytobrush and assessed whether the strength of association between periodontitis and HPV is modified by the collection method. Data from a cross-sectional study of Hispanic adults in Puerto Rico (n = 346) who provided oral rinse and cytobrush samples for oral HPV detection and were clinically evaluated for periodontitis. The agreement between the oral mouthwash and cytobrush methods was assessed using the Kappa (κ) statistic. Logistic regression models were used to determine if the association between HPV infection and other risk factors varied by oral sample collection method. HPV prevalence was slightly higher using cytobrush than oral rinse (5.8% vs. 4.3%). The sensitivity of cytobrush to detect oral HPV was 64.7%, and the specificity was 97.4%. We observed a κ of 0.61 (95% confidence interval [CI]: 0.45-0.78), indicative of fair to good agreement between the two collection methods. The association between oral HPV infection and periodontitis severity was stronger when using the oral rinse collection method (odds ratio [OR] = 3.23, 95% CI: 1.06-9.84); the association was not statistically significant for cytobrush (OR = 1.96, 95% CI: 0.68-5.65). These findings support the significance of choosing the most suitable collection method in oral HPV-related studies. Selecting the most appropriate collection method is an essential criterion in oral HPV-related studies.