Serum HDL-C level was associated with the genetic polymorphism of CD36, SCARB1 and MFSD2A. T2DM patients with CD36 rs1049673 (CG, GG), CD36 rs1054516 (CT), CD36 rs2151916 (TT, CT), SCARB1 rs5888 (GG), MFSD2A rs12083239 (GG, CG), MFSD2A rs4233508 (TT) and MFSD2A rs12072037 (CA, AA) genotypes had lower HDL-C level than the control ones (P < 0.05). The gene discussed is MFSD2A; the disease is type 2 diabetes mellitus.