To determine the presence and the morphological features of bacterial biofilms in surgical specimens of patients with chronic rhinosinusitis (CRS) compared with control patients without CRS by scanning electron microscopy (SEM), and to evaluate the role of biofilm on the pathogenesis of CRS. Fifteen patients with CRS undergoing endoscopic sinus surgery and 11 control patients with fracture of nasal bone were enrolled in this study. Clinical information was recorded from each patient. All patients underwent a thorough otolaryngological examination, preoperative paranasal sinus computerized tomography (CT) scanning which were evaluated according to the Lund-Mckay CT scoring system. All the samples including uncinate process, ethmoid mucosa from CRS group and uncinate process, ethmoid bulla from control group were prepared using standard methods for SEM. The presence of bacterial biofilms on the samples of two groups was observed by SEM. Statistical analysis was performed using SPSS 13.0. Continuous data was analyzed by Student t test and dichotomous data was analyzed by chi² or Fisher exact test. P was considered to be significant at a level of 0.05. Nine (60.0%) of the 15 patients were found to have evidence of biofilms. In control group, only 1 (9.1%) of 11 patients had biofilm. The difference was statistical significant (chi² = 6.949, P < 0.01). All controls except one had healthy appearing cilia and goblet cells without biofilms. All the 16 CRS patients showed aberrant findings of the mucosal surface with variation in degrees of severity from disarrayed cilia to complete absence of cilia and goblet cells. Among them the typical morphologic feature such as water channels, 3-D structure, and matrix-embedding spherical or elliptical bodies were noted in 9 cases. Five samples including one case from control showed cilia aggregation. The preoperative CT scores of the CRS patients with biofilms (n = 9) were significantly higher than those without biofilms (n = 6, t = 2.14, P < 0.05). The typical morphologic feature of BF such as water channels, 3-D structure, and matrix-embedding spherical or elliptical bodies were noted in sinus mucosa of patients with CRS by the SEM. The positive rate of bacterial biofilms in CRS group was significantly higher compared to control group, which indicated bacterial biofilms might play an important role in the pathogenesis of CRS. Besides the typical bacterial biofilm features, cilia aggregation was found in five cases of CRS patients. We consider cilia aggregation can be regarded as one morphologic feature of bacterial biofilm in nasal mucosa, which needs further study. The presence of bacterial biofilms in CRS patients is associated with paranasal CT scores, which indicates that bacterial biofilm is correlated with the severity of CRS.