BACKGROUND: Impaired fasting glucose (IFG) is more prevalent in men, whereas impaired glucose tolerance (IGT) is more prevalent in women. AIM: To determine whether gender difference in the prevalence of glucose intolerance is related to height. METHODS: A cross-sectional study of 2,368 first-degree relatives (FDR) of patients with type 2 diabetes was conducted between years 2003 to 2005. All participants (614 men and 1754 women) were in the age range 30-60 years, and were FDR of consecutive patients from outpatient clinics at Isfahan Endocrine and Metabolism Research Centre, Iran. All subjects underwent a standard 75 g 2-h oral glucose tolerance test (OGTT). Weight, height, waist and hip circumference, and glycated haemoglobin were also measured. RESULTS: IGT was more common amongst women (OR 0.66; 95% CI 0.51, 0.87),whereas diabetes (OR 1.31; 95% CI 0.96, 1.78), and IFG (OR 1.41; 95% CI 1.10, 1.80) was more common amongst men. Women had a lower mean fasting plasma glucose (FPG) (p < 0.001), but showed higher 2hPG, and FPG-2hPG increase (p < 0.001). The gender difference in mean 2hPG and FPG2hPG increase, was not evident after adjustment for height. Negative correlation to height was observed in 2hPG and FPG-2hPG increase, both in men and women (p < 0.001), but height showed little association with FPG. CONCLUSIONS: Women had higher mean 2hPG and FPG-2hPG increase, but showed a lower FPG level than men. The inverse association between height and 2hPG and FPG-2hPG increase may be explained by gender difference.