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Aims The relationship between adiponectin and type 2 diabetes mellitus (T2DM) is established; however the evidence on its role in high-density lipoprotein (HDL) functionality is still scant. The aim of this study was to assess the association of adiponectin with HDL functionality especially on the antioxidant capacity and HDL subfractions in individuals with T2DM. Methods This case-control study enrolled 356 individuals who were divided into two groups: diabetics [T2DM (n = 188)] and non-diabetic [nT2DM (n = 168)]. The association of adiponectin level on HDL functionality parameters was done in function of the cut-off point for adiponectin [percentile p Results Body mass index (BMI), waist circumference (WC) and body fat mass (FM) were higher in T2DM. The larger HDL particles (HDLLARGE) were lower in T2DM group in comparison with nT2DM (28.20% versus 30.40%; p = 0.016). Individuals with T2DM and simultaneous highest adiponectin (p ≥ 75) had 2.25 OR (95% CI = 1.03–4.91) and 5.14 OR (95% CI = 2.37–11.15) to present higher HDL-C and HDLLARGE concentrations. After adjustment for multiple confounders, high level of adiponectin was independently related with improvement of the HDL antioxidant capacity (OR = 2.78; 95% CI = 1.16–6.67). Conclusions High adiponectin level associates with a lesser negative impact of T2DM on HDL functionality by increase in APO AI, particles size, and cholesterol content. On the same token, higher adiponectin was associated with greater odds to have high antioxidant capacity.