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Objective Polycystic ovary syndrome (PCOS) is a chronic ovulation disorders and is characterized by hyperandrogenism and continuous anovulation. The objective is to discuss the application of Fishier discriminant analysis (FDA) on Chinese medicine syndrome type distribution in patients with PCOS and the relationship with sexual hormones between the symptoms. Methods Chinese medicine syndrome types of 62 PCOS patients were differentiated，including 21 cases with kidney deficiency syndrome，22 cases with kidney deficiency and phlegm stagnation syndrome and 19 cases with kidney liver depression syndrome. These cases covered single symptoms，accompanied symptoms and are separated with the method of twice grouping. The cases with kidney deficiency syndrome were separated with Logistic regression first，and then the remaining accompanied symptoms were for the second classification with Fishier discriminant analysis method. The correlation on sex hormones between the symptoms was analyzed with statistical method. Results Fishier discriminant analysis was used for the separation of accompanied symptoms and the correct rate was 87.8%. The luteinizing hormone (LH) level was significantly higher in the groups of kidney deficiency and phlegm stagnation syndrome than in the group of kidney liver depression syndrome（P＜0.05）and the prolactin (PRL) level was significantly higher in the group of kidney liver depression syndrome than in the group of kidney deficiency and phlegm stagnation syndrome (P＜0.05). Conclusions The test results of Fisher discriminant function model are in good agreement with those obtained from the actual situation，and may be used as an auxiliary tool for the exploration on Chinese medicine syndrome type distribution in patients with PCOS. There is a correlation between syndrome type and sexual hormone levels.