Background: The between-subject variability in diabetes risk persists in epidemiological studies, even after accounting for obesity. We investigated whether the humero-femoral index (HFI) was associated with prevalence of type 2 diabetes mellitus (T2DM) and assessed the incremental value of HFI as a marker of T2DM.Methods: This population-based cross-sectional study used data from the National Health and Nutrition Examination Survey from 1999 to 2018. We assessed 42,088 adults aged ≥ 30 years. HFI was defined as the upper arm length/upper leg length ratio. The outcome included undiagnosed diabetes (based on 2-hour plasma glucose levels, fasting glucose and hemoglobin A1C) and history of diabetes (diagnosed diabetes or taking antidiabetic drugs).Results: As compared with the bottom quartile, the prevalence ratio of T2DM was 1.28 (95% CI 1.19–1.38) in the second, 1.61 (95% CI 1.50–1.72) in the third, and 1.75 (95% CI 1.64–1.88) in the fourth quartile of HFI (P for trend < 0.0001). The positive association remained consistent within different patterns of BMI and WC in men but was rendered null in women. After adding HFI to the reference model (including WC only), the discrimination slopes increased by 60.0% in men and 51.1% in women.Conclusion: Our findings suggest that HFI may be a key component in body structure contributing to the risk of T2DM. In men, the highest HFI was associated with elevated prevalence of T2DM, independent of BMI and WC.