Body composition differs between men and women, with women having proportionally more fat mass and men more muscle mass. Although men and women are both susceptible to obesity, health consequences differ between the sexes. The purpose of our study was to assess sex differences in body composition using anatomic and functional imaging techniques, and its relationship to cardiometabolic risk markers in subjects with overweight/obesity. After written informed consent, we prospectively recruited 208 subjects with overweight/obesity who were otherwise healthy (94 men, 114 women, age 37 ± 10 years, BMI 35 ± 6 kg/m2). Subjects underwent dual-energy X-ray absorptiometry (DXA) and computed tomography (CT) for fat and muscle mass, proton MR spectroscopy (1H-MRS) for intrahepatic (IHL) and intramyocellular lipids (IMCL), an oral glucose tolerance test, serum insulin, lipids, and inflammatory markers. Men and women were compared by Wilcoxon signed rank test. Linear correlation and multivariate analyses between body composition and cardiometabolic risk markers were performed. Women and men were of similar mean age and BMI (p ≥ 0.2). Women had higher %fat mass, extremity fat, and lower lean mass compared to men (p ≤ 0.0005). However, men had higher visceral adipose tissue (VAT) and IMCL and higher age-and BMI-adjusted IHL (p < 0.05). At similar age and BMI, men had a more detrimental cardiometabolic risk profile compared to women (p < 0.01). However, VAT in women, and IMCL in men, were more strongly associated with cardiometabolic risk markers, while more lower extremity fat was associated with a more favorable cardiometabolic profile in women compared to men (p ≤ 0.03). Although the male pattern of fat distribution is associated with a more detrimental cardiometabolic risk profile compared to women of similar age and BMI, VAT is more strongly associated with cardiometabolic risk markers in women, while IMCL are more detrimental in men. Lower extremity fat is relatively protective, in women more than in men. This suggests that detailed anatomic and functional imaging, rather than BMI, provides a more complete understanding of metabolic risk associated with sex differences in fat distribution.