Obesity seems to be associated to migraine headache. Increase in body fat, especially in gluteofemoral region, elevates adiponectin and leptin secretion which in turn impair inflammatory processes that could be contributing to migraine risk. This study was designed to assess the relationship between body composition and risk of migraine for the first time. In this cross-sectional study, 1510 middle-aged women who were visited in a weight reduction clinic of university were recruited. Migraine was diagnosed with HIS criteria. Body composition parameters including total fat mass (FATM), total fat free mass (FFM), truncal fat mass (TFATM), and truncal fat free mass (TFFM) was assessed using bioelectric impedance. We further assessed cardiovascular risk factors and smoking as confounding factors. To determine the real association between different variables and risk of migraine, the associations were adjusted by multivariate logistic regression analysis. Elevation in fasting blood sugar, total cholesterol, LDL cholesterol, FFM, TFFM, and waist-to-hip ratio increased the risk of migraine. When the associations were adjusted for other factors, only the association between migraine and FFM remained statistically significant. Lower FFM increased the risk of migraine in overweight and obese individuals. In the other words, higher fat free mass could be a protective factor for migraine.