Objective:  Obesity is strongly associated with metabolic syndrome, but not all obese individuals display a clustering of metabolic risk factors. Recent studies have shown that in vitro subcutaneous (SC)-preadipocyte differentiation is negatively associated with obesity. These results suggest that impaired adipogenesis is an important factor linking obesity to metabolic disorders. We examined whether in vitro preadipocyte differentiation is associated with metabolic syndrome, independent of obesity. Design/patients/measurements:  Paired adipose tissue samples were obtained from the 13 non-obese women and the 65 obese women. The CD34(+) /CD31(-) cells were isolated from the stromal vascular fraction of both SC- and omental (OM)- fat depots by immune magnetic separation, and the subset was cultured with a differentiation cocktail. Then, we analyzed the relationship between the degree of preadipocyte differentiation and metabolic factors. Results:  Obese women without metabolic syndrome (n = 37) had significantly higher SC-preadipocyte differentiation than equally obese women with metabolic syndrome (n = 28); however, OM-preadipocyte differentiation was similar in both groups. SC-preadipocyte differentiation was strongly correlated with triglycerides, HDL-cholesterol, homeostasis model assessment of insulin resistance, and OM-adipocyte size. However, OM-preadipocyte differentiation was not correlated with any of these parameters. Conclusions:  This study identified that SC-preadipocyte differentiation is associated with metabolic syndrome independent of obesity, whereas OM-preadipocyte differentiation is not. These findings suggest that, in the setting of obesity, an enhanced adipogenic capacity of SC-depots could be protective for metabolic syndrome. Our data underscores an interaction between adipose tissue homeostasis and metabolic disorder.