Inverted papillomas (IPs) are the most frequent type of sinonasal papillomas. These benign but destructive lesions are known for their high recurrence rate, probably due to incomplete excision. Our aim was to investigate the frequency of human papillomavirus (HPV) infection in patients with IPs and in IPs associated with squamous cell carcinoma (IPsSCC) and to compare it with the frequency of HPV infections in the control group. The influence of HPV infection on the malignant alteration and recurrence rate of IPs was also evaluated. Paraffin-embedded tissue samples from 68 patients with sinonasal IPs and 5 patients with IPsSCC were analyzed in this retrospective study. The control group consisted of 47 patients who had undergone septoplasty or mucotomy of the inferior turbinate. PCR amplification with consensus primer sets was performed to detect alpha-HPVs, and direct sequencing of the PCR products with the same primers was used to determine the HPV genotypes in the samples. We detected HPV DNA in 20 (30.3%) patients with IPs, in 3 (60%) patients with IPsSCC, and in 6 (13%) patients from the control group. The frequency of HPV infection in the study group was statistically significantly higher (p = 0.032) than in the control group. The presence of HPV DNA was not a statistically significant predictor of the recurrence of IPs (p = 0.745) nor was it a statistically significant risk factor for associated SCC (p = 0.32). Since HPV type 11 was the predominant genotype in the IPs, IPsSCC, and in the control cases, we presume that HPV infection may represent incidental colonization rather than being an important etiological factor of IPs.