Objective · To identify the differential proteins from follicular fluid of patients with polycystic ovarian syndrome (PCOS) employing protein chip array, and provide a theoretical basis for further study of PCOS. Methods · AAH-BLG-507 array was used to test the follicular fluid of 6 PCOS patients with normal body mass index (BMI) and 6 non-PCOS controls with age and BMI-matched. The differential proteins were identified and bioinformatics analysis was carried out by functional annotation analysis, KEGG pathway analysis and protein-protein interaction network analysis. Results · Compared with non-PCOS controls, 25 up-regulated proteins and 49 down-regulated proteins were identified from follicular fluid of patients with PCOS. The classification of differential proteins based on molecular function revealed that they were mainly involved in cytokine activity and chemokine activity. KEGG pathway analysis was performed and pathways associated with cytokine-cytokine receptor interaction and chemokine signaling pathway were significantly enriched. The core proteins filtered by protein-protein interaction network analysis were mainly chemokines and their receptors. Conclusion · Protein chip array can be used to establish the differential expressed protein profile from follicular fluid of patients with PCOS. The cytokine-cytokine receptor interaction and chemokine signaling pathway may be involved in the pathogenesis of PCOS.