Inverted papillomas are rare tumors of the nasal cavity and paranasal sinuses. These tumors are commonly regarded as benign lesions; nevertheless, malignant transformation occurs in up to 13% of cases. In the present retrospective study, specimens from 21 patients with inverted papillomas of the paranasal sinuses and the nasal cavity were investigated in order to analyze the distribution of genetic imbalance and to classify chromosomal aneuploidy in these tumors as a predictor for their biological behavior. Currently, human papilloma viruses (HPVs) are accepted as tumor-inducing and -promoting agents involved in benign and malignant tumors of mucosal tissues in the upper aerodigestive tract. To date more than 80 HPV types have been identified by differences in the nucleotide sequences. Several types (e.g., HPV16, HPV18) are associated with an increased risk for developing cancer. Other types (e.g., HPV6/11) are identified more frequently in benign lesions of stratified mucous membranes. We detected HPV genomes by universal and specific primer polymerase chain reaction. Using degenerated primers derived from the L1 major envelope gene, an amplification of HPV DNA fragments of the correct size was observed in 7 of 21 cases. In one specimen, where an inverted papilloma associated with a squamous cell carcinoma was histologically confirmed, HPV18-specific primers detected the HPV18 genome. The tumors in which an amplification of HPV DNA fragments were observed showed the highest proliferation scores along with the highest rate of aneuploid cells detected by quantitative DNA analysis.