The aim of this study was to compare the effects of metformin and GnRH analogues on lipid metabolism and hormonal parameters in women with polycystic ovary syndrome (PCOS). The study population consisted of 40 women with PCOS. Patients were divided into two groups. Metformin (850 mg, two times per day) was administered to the first group and GnRH analogue (goserelin 3.6 mg, every 28 days) was given to the second group. Only 32 women completed the study and their results were evaluated. Insulin resistance was not ascertained in patients. Metformin treatment resulted in a significant decline in mean body mass index, body weight and circumferences of waist and hip. In addition, there was a significant decrease in LH levels and a significant increase in FSH, progesterone and sex hormone binding globulin (SHBG) concentrations. Although there was an improvement in lipid abnormalities, no changes in starving glucose and insulin levels were observed. GnRH analogue resulted in a significant increase in FSH and SHBG levels and a significant decrease in LH, total testosterone, DHEAS levels and LH to FSH ratio. In patients treated with GnRH analogue, there was an improvement in lipid metabolism but there was no change in clinical features. Metformin and GnRH analogue use appears to improve endocrinological features and lipid abnormalities which consequently result in cardiovascular diseases in PCOS, independent from insulin resistance.