Human papillomavirus (HPV) infection is a significant risk factor for uterine cervical carcinoma. Many studies have also demonstrated the presence of HPV in oral epithelia tissue, but the role of HPV infection in oral squamous cell carcinoma (OSCC) is still controversial. The aim of this study was to determine the frequency and type of HPV in OSCC and oral pre-cancerous lesions. DNA samples were collected by cytobrushing from 51 patients with OSCC, 46 with oral pre-cancerous lesions and 90 normal controls. Nested polymerase chain reaction and gene-chip arrays were used to identify the HPV types in the samples. In pre-cancerous lesions, there was a higher frequency of HPV of any type (14/46, OR = 2.844, CI = 1.186-6.816, P = 0.0216) and of low-risk HPV types (9/46, OR = 5.529, CI = 1.597-19.14, P = 0.0096) than in control samples. The prevalence of high-risk types was significantly higher in OSCC than in control lesions (11/51 vs 8/90, OR = 2.819, CI = 1.051-7.558, P = 0.0420) but this was not the case for HPV of any type (13/51 vs 12/90, OR = 2.244, CI = 0.9266-5.337, P = 0.1066). High-risk HPV types are prevalent in OSCC and may play a role in its progression, while low-risk types are associated with oral pre-cancerous lesions.