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In order to investigate the pathological characteristics of polycystic ovaries diagnosed by transvaginal ultrasound (TVS) in patients with polycystic ovarian syndrome (PCOS) and to investigate the relationship between morphological and endocrine changes in the ovaries, 32 PCOS patients with bilateral polycystic ovaries (> 10 cysts) detected by TVS were studied; 20 ovulatory women served as controls. Ovarian tissues from wedge resection were examined histologically. A comparative histological and TVS study of ovarian morphology was made, and the relationship between the number of small cysts and the endocrine profile was examined. The position and size of small cysts on TVS agreed with those observed histologically. There was a significant correlation between the number of small cysts on TVS and the number of atretic follicles with hypertrophied and luteinized inner theca cells, and thickened ovarian capsules. Numerous atretic follicles and thickened ovarian capsules were observed in 97 and 64% of ovaries respectively, from PCOS patients. In patients with PCOS, a significant positive correlation was noted both between the number of small cysts and delta 4-androstenedione (ASD), and between ASD and the luteinizing hormone/follicle-stimulating hormone (LH/FSH) ratio. Furthermore, testosterone, ASD and the number of small cysts on TVS were significantly higher in PCOS patients with ovarian thickened tunica compared to PCOS patients without ovarian thickened tunica. TVS images of ovaries in patients with PCOS correlated with the histopathological and endocrine features. It is suggested that an increase in intra-ovarian small cysts leads to increased production of ovarian androgen, in turn influencing the secretion of gonadotrophin, and is correlated with ovarian capsular thickness.