Background: Chronic rhinosinusitis (CRS) can be divided to CRS without nasal polyps (CRSsNP) and eosinophilic and non-eosinophilic CRS with nasal polyps (CRSwNP). There is little evidence on the efficacy of glucocorticoids and macrolides in different phenotypic patients. The aim of this study was to compare the benefit of glucocorticoids and macrolides following endoscopic sinus surgery (ESS) in different phenotypic CRS. Methods: This study was a prospective single-blind comparative effectiveness trial. A total of 187 Chinese patients with CRS were stratified to CRSsNP and eosinophilic and non-eosinophilic CRSwNP group and then randomized to receive fluticasone propionate nasal spray at 200 mu g or clarithromycin tablet at 250 mg once daily for 3 months after ESS. Oral prednisone was given as a rescue therapy after the stop of study medication. Patients were assessed before ESS and 1, 3, 6 and 12 months after dosing. Symptom severity was scored by patients using visual analog scale method and endoscopic findings were scored by the senior physician blinded to treatment according to European Position Paper on Rhinosinusitis and Nasal polyps 2012. Results: The total and individual symptom scores, and total and individual endoscopic domain scores were reduced significantly after ESS in both medication groups, whereas no significant difference was observed for two medications at most follow-up visits in each subtype of CRS. No difference in the frequency of subjects with rescue therapy or refractory CRS was found between two medication groups either. Conclusions: We could not show significant difference of effect between fluticasone propionate and clarithromycin in the postoperative treatment for CRSsNP and eosinophilic and non-eosinophilic CRSwNP patients.