Objective: The objective was to investigate the relationship between insulin resistance and increased serum homocysteine in women with polycystic ovarian syndrome (PCOS). Design: Prospective controlled trial. Setting: Department of Obstetrics & Gynecology, Mansoura Faculty of Medicine, Mansoura, Egypt. Patients: Ninety PCOS women as a study group and 35 women with infertility due to other causes as a control group. Outcome measures: Serum homocysteine levels in the presence and absence of insulin resistance in PCOS patients. Results: Homocysteine levels were significantly higher in PCOS patients than in the controls. Considering 11 mu mol/l as the cut-off level for a normal homocysteine level, 41.1% of PCOS patients (37 out of 90) and 2.9% of control group (1 out of 35) had high homocysteine levels. With regard to insulin resistance, 23% of PCOS patients without insulin resistance (9 out of 39) had a high homocysteine level, while 47% of PCOS patients with insulin resistance (24 out of 51) had this, thus demonstrating the effect of insulin resistance on the homocysteine level. Conclusion: There is a strong association between serum homocysteine and insulin resistance in women with PCOS that contributes to the long-term complications of PCOS. (c) 2006 Elsevier Ireland Ltd. All rights reserved.