Aim To investigate the association between high density lipoprotein (HDL) subclasses and Omentin-1 concentration in metabolic syndrome (MS). Methods Concentrations of plasma lipids and the apolipoproteins in the MS subjects (n=102) and healthy controls (n=81) were detected by automated biochemical analyzer. The levels of Omentin-1 were determined by enzyme-linked immunosorbent assay (ELISA) kits. The contents of plasma HDL subclasses were determined by two dimensional gelelectrophoresis-immunodetection. According to the level of plasma Omentin-1, the MS subjects were divided into three layers amount (low Omentin-1 group (Omentin-1≤9.10 μg/L), middle Omentin-1 group (9.10 μg/L100/AⅠ and LDLC/HDLC were significantly increased in MS patients (P<0.05 or P<0.01). Meanwhile, the concentrations of high density lipoprotein cholesterol (HDLC), apolipoprotein AⅠ (apoAⅠ) were significantly decreased in MS patients (P<0.05 or P<0.01). Compared with the low Omentin-1 group, preβ₁-HDL and HDL_3b were decreased (P<0.05 or P<0.01), while the HDL_2a were increased significantly in high Omentin-1 group (P<0.05). Conclusion The levels of plasma Omentin-1 were decreased in MS patients, and the particle size of HDL showed a shift toward smaller size.The low plasma Omentin-1 may be related to HDL subclasses distribution abnormality and dyslipidemia.