Aim To investigate the relationship of plasma homocysteine (Hcy) level and genetic polymorphisms of methylenetetrahydrofolate reductase (MTHFR) C677T and cystathionine β-synthase (CBS) T833C related to homocysteine metabolism with carotid intima-media thickness (IMT) in type 2 diabetic patients. Methods Plasma Hcy level was measured by enzyme linked immunosordent assay (ELISA). MTHFR genetic C677T polymorphism was determined by polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP), and CBS T833C polymorphism was determined by amplification refractory mutation system (ARMS) method, carotid intimal-medial wall thickness was determined by the use of the duplex ultrasonography. Results The genotype frequency of diabetics with thicked IMT was different from that of diabetic patients with normal IMT and control groups (p<0.05). Plama homocysteine levels were markly higher in patients with MTHFR or CBS genetic mutation than those in patients without mutation in each group. IMT in MTHFR or CBS genetic mutation were thicker than those in patients without mutation in diabetic group. Conclusion Mutation of MTHFR or CBS can both cause the elevation of plasma homocysteine level so as to induce the onset of arteriosclosis in diabetics. Their genetic mutations are possibly the important mechanism of macroangiopathy in diabetics.