Objective To evaluate association of plasma levels of homocysteine, folate and vitamin B12 as well as genetic polymorphisms of homocysteine with ulcerative colitis (UC). Methods Three hundred and ten consecutive patients with UC and 936 healthy controls were recruited.Polymorphisms of methylenetetrahyrdofolate reductase (MTHFR, C677T and A1298C), methionine synthase (MTR) A2756G and methionine synthase reductase (MTRR) A66G were genotyped using PCR-RELP methods. Eighty eight patients and one hundred healthy controls were randomly selected for determination of plasma levels of homocysteine by enzymatic cycling assay, and concentrations of folate and vitamin B12 were measured by corpuscle immune chemiluminescence assay. Results The variant allele and genotype frequencies of MTHFR 1298C, MTR 2756G and MTRR 66G were significantly higher in UC patients than in the healthy controls (P＜0. 01). Moreover, plasma homocysteine level was obviously higher in UC patients than in controls [(21.73±6.59) mmol/L vs(12.47±5.01)mmol/L,P<0.01).Whereas both folate F(11.25±6.19)nmol/L] and vitamin B12 [(322.81±128.47)pmol/L] concentrations were significantly lower in UC patients than in controls [(15.28±7.72)nmol/L and (422.59±129.36)pmol/L,respectively,P<0.01].Logistic analysis revealed that abnormal levels of homocysteine,folate and vitamin B12 were independent risk factors for UC(P<0.01).Conclusions Plasma levels of homocysteine,folate and vitamin B12 as well as the related genetic polymorphisms of homocystein are correlated with UC,which provides a theoretical basis for supplement of folate and vitamin B12 in treatment of UC patients.