BACKGROUND: Elevated levels of plasma homocysteine (Hcy) have been implicated as a significant risk factor for cardiovascular disease. Although long-term treatment with metformin can increase Hcy levels in patients with type II diabetes mellitus or coronary heart disease, it is becoming an increasingly accepted and widespread medication in polycystic ovary syndrome (PCOS). In the literature, only one study has demonstrated that metformin increases Hcy levels in PCOS patients, but the effect of other insulin sensitizers on Hcy levels have not been reported previously in women with PCOS. We aimed to assess the effects of metformin and rosiglitazone on plasma Hcy levels in patients with PCOS. METHODS: Thirty women were randomized to two groups: 15 women in group 1 received 850 mg of metformin twice daily for 3 months. In group 2, 15 women received 4 mg of rosiglitazone for 3 months. In both groups, body mass index, menstrual pattern, and plasma total Hcy, insulin, glucose and lipid metabolism parameters were recorded at baseline and at 3 months. RESULTS: Hcy levels increased from 8.93 +/- 0.49 to 11.26 +/- 0.86 mu mol/l (P=0.002) and from 10.70 +/- 0.86 to 12.36 +/- 0.81 mu mol/l (P=0.01) in the metformin and rosiglitazone groups, respectively. Apolipoprotein (Apo) A1 levels increased from 127.10 +/- 6.85 to 145.7 +/- 7.18 mg/dl (P=0.018) in the metformin group. Total cholesterol (total-C), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), lipoprotein (a) and Apo B levels decreased in the metformin group, but the change was not significant. Total-C levels decreased from 161.15 +/- 8.94 to 150.23 +/- 8.73 mg/dl (P=0.026), HDL-C decreased from 43.13 +/- 2.65 to 39.15 +/- 2.52 mg/dl (P=0.005) and LDL-C levels decreased from 93.83 +/- 6.06 to 80.7 +/- 2.30 mg/dl (P=0.021) in the rosiglitazone group. CONCLUSION: Treatment with insulin sensitizers in women with PCOS may lead to increases in Hcy levels.