The objectives of this study were to: I) discover novel human papillomaviruses (HPVs) using next generation sequencing (NGS) technology in oral rinse samples collected from oral cavity cancer (OCC) and oropharyngeal cancer (OPC) patients; II) determine the prevalence of novel HPVs in archived OCC and OPC tissue samples; and III) examine the frequency of novel oncogenic HPVs in cancer and non-cancer oral rinse samples using real-time PCR. Oral rinse samples were collected from 100 head and neck cancer patients, and 110 healthy individuals. NGS techniques were used to detect novel HPVs. Three potentially new types of HPV were discovered. Novel virus (NV) 14.4 was closely related to HPV76 with an 89% homology and is a member of the genus Beta-papillomavirus (β-PV); NV69.1 was distantly related to the genus Alpha-papillomavirus (α-PV), and NV95 was closely related to HPV147 with a 65-77% homology and is part of the genus Gamma-papillomavirus (γ-PV). In archived oral tissue samples, NV14.4 was detected in a single patient with OCC. Of the oral rinse samples, NV69.1 was more prevalent than the other two NVs. Our results demonstrated that there are novel HPVs present in oral rinse samples that may be associated with OCC and OPC. These novel HPVs can be identified and characterized using NGS techniques.