Aim: The aim of this study was to determine the prevalence of HPV in odontogenic cysts. Materials & Methods: The DNA of 85 samples of odontogenic cysts consisted of odontogenic keratocyst (OKC), dentigerous cyst (DC), calcifying odontogenic cyst (COC) and periapical cyst were extracted. Amplification of HPV genes were performed using GP5+/GP6+ primers. The results were statistically analyzed using chi-square test. Results: Three samples (15%) of periapical cysts, 4 samples (20%) of OKCs, 5 samples (25%) of DCs and 7 samples (28%) of COCs (9.09% of type Ia, none of type Ib, 66.6% of type Ic and 50% of type II) were HPV-positive. Statistical analysis showed that the frequency of HPV DNA was significantly different only between type Ia and Ib of COC samples. Conclusion: The high prevalence of HPVs in odontogenic cysts proposed that these microorganisms may have a potential role in the pathogenesis of odontogenic lesions. Clinical significance: Recognition of etiologic and predisposing factors of odontegenic lesions could introduce new approaches in the management of these lesions. Due to the possible role of HPV in the pathogenesis of odontogenic lesions, antiviral therapy has the potential to be considered as an adjunctive treatment to reduce the recurrence rate after surgical procedure.