Objective To explore the relationship between the bacterial biofilm, allergy,inflammatory cytokines and refractory rhinosinusitis. Method According to the assessment of symptom by visual analogue scale and nasal endoscopy by Lund-Kennedy system, 19 patients with persistent chronic rhinosinusitis and 6 patients with curative chronic rhinosinusitis were recruited from 340 chronic rhinosinusitis patients underwent functional endoscopic sinus surgery for the first time and received standard medication postoperatively. These cases were divided into the study group and the control group respectively.Electron microscope scanning and enzyme linked immunosorbent assay were used to observe the bacterial biofilm formation on ethmoid sinus mucosal surface and detect the concentration of specific IgE and interleukin (IL) 4, IL-5, IL-6, and IL-8 in ethmoid sinus mucosal tissue. Then the differences between the group were all found biofilm formation in ethmoid sinus, besides the damage of epithelial cells and cilia. Six cases from the control group were found no biofilm, with the integrity of epithelial cells and cilia. Statistical Specific IgE: specific IgE was detected in nine cases from the study group and was not found in any case all detected under normal value both in the study group and the control group, except for only 2 cases from the study group with higher IL-8 concentration. Positive reaction to IL was detected as follows: IL-4 (7cases), IL-5 (14 cases), IL-6 (15 cases), and IL-8 (12 cases) in the study group; IL-4 (1 case), IL-5 (5 cases), IL-6 (5 cases), and IL-8 (5 cases) in control group. No difference in IL detection rate was found between the two groups (P > 0.05). Conclusion Bacterial biofilm and allergic inflammation are important factors resulting into refractory chronic rhinosinusitis.