BACKGROUND: The aim of the current study was to assess the effects of B-group vitamins and folic acid administration on serum levels of homocysteine (Hcy) in patients with polycystic ovarian syndrome (PCOS) on short-term metformin treatment. METHODS: Patients were randomly assigned to one of three treatment groups. Group 1 patients (n=20) received metformin (850 mg twice daily); group 2 patients (n=20) received metformin (850 mg twice daily) and B-group vitamins (vitamin B-1, 250 mg; vitamin B-6, 250 mg; vitamin B-12, 1000 mu g twice daily); and group 3 patients (n=20) received metformin (850 mg twice daily) and folic acid (174 mu g twice daily). In all groups, lipid profiles and plasma total Hcy, vitamin B-12, folic acid and glucose levels were recorded at baseline and at 3 months. RESULTS: A 26.5% increase in Hcy levels was seen after 12 weeks of metformin therapy, while 21.17 and 8.33% decreases in Hcy levels were detected when B-group vitamins or folic acid plus metformin were given respectively. There were no statistically significant differences recorded in insulin sensitivity using homeostasis model assessment in the three groups. CONCLUSION: These findings suggest that B-group vitamins and folic acid administration counteract the Hcy-increasing effect seen with metformin therapy.