Fat distribution is strongly associated with insulin resistance, a risk factor for type 2 diabetes and cardiovascular diseases. However, associations of different adipose tissue depots or/and obesity indices with insulin resistance have not been systematically evaluated. In this study we examined associations of different adipose tissue depots/obesity indices with insulin resistance, as measured by homeostatic model assessment of insulin resistance (HOMA-IR) in observational studies. A total of 40 studies with 56 populations and 29 adipose tissue depots/obesity indices were included in the meta-analysis. There were strong correlation between HOMA-IR and visceral fat mass (r = 0.570, 95% confidence interval(CI): 0.424~0.687), total fat mass (r = 0.492, 95%CI: 0.407~0.570), body mass index (r = 0.482, 95%CI: 0.445~0.518) and waist circumference (r = 0.466, 95%CI: 0.432~0.500), except lower extremity fat (r = 0.088, 95%CI: -0.116~0.285). Sample size, diabetic status, gender, mean of body mass index, and race contributed to heterogeneity of these associations. This study showed a positive correlation between insulin resistance and most adipose tissue depots/obesity indices, and the strongest association is for visceral fat mass.