Genetic alterations, such as microsatellite instability (MSI) and loss of heterozygosity (LOH), have been detected in various inflammatory diseases, providing evidence that acquired somatic mutations might play a role in the aetiopathogenesis of chronic inflammatory conditions. The aim of this study is to assess the presence of MSI and/or LOH in nasal cytology of patients with nasal polyps. Prospective case-controlled basic science experiment utilizing human blood and human nasal brush samples. Nasal brush samples and peripheral blood from 12 patients with nasal polyps were analyzed. DNA was extracted and analyzed for MSI and LOH using the following microsatellite markers: D2S2113, D6S344, D6S1002, D11S1253, D11S480, USAT24G1, and D13S273, harboring potential susceptibility genes for nasal polyposis. Microsatellite DNA analysis was also performed in 7 control subjects. MSI or LOH were revealed in 3 specimens of the nasal polyps group. Among these there were 2 cases of LOH, one for marker D11S1273 and one for D13S273, and one case of MSI in marker USAT24G1. Each one of these alterations was detected in a different patient. None of the control subjects exhibited any genetic alterations in the 7 markers tested. This is the first time that microsatellite genetic alterations are reported in nasal disease. The presence of such alterations suggests that acquired genomic somatic mutations might play a role in the pathogenesis of nasal polyps.