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It has been reported that abnormal elevation of homocysteine is quite prevalent in ulcerative colitis (UC) patients. We attempted to explore the relationship of UC with transcobalamin II (TCN2) gene polymorphisms and serum homocysteine, vitamin B, and folate levels in Chinese patients. TCN2 (rs1801198, rs9606756) genotypes were detected by the improved multiple ligase detection reaction (iMLDR) technique in 527 UC patients and 574 controls. Moreover, 128 UC patients and 138 controls were randomly selected for the measurement of homocysteine, vitamin B, and folate levels by enzymatic cycling assay or chemiluminescence immunoassay. For TCN2 (rs1801198), the frequency of allele G and combined frequencies of CG and GG genotypes were increased in patients with mild, moderate, and severe UC compared with those with remission UC (all P < 0.001). The average homocysteine level was elevated (10.78 ± 3.33 vs 9.91 ± 2.88 μmol/L, P = 0.024), whereas the average vitamin B and folate levels were reduced (408.66 ± 185.00 vs 457.42 ± 206.47 pg/mL, P = 0.044; 6.81 ± 3.06 vs 8.17 ± 2.58 ng/mL, P < 0.001, respectively) in UC patients than in controls. Compared with controls, the prevalence of hyperhomocysteinemia (HHcy >15.0 μmol/L), vitamin B deficiency (<203.0 pg/mL), and folate deficiency (<4.0 ng/mL) was higher in UC patients (all P < 0.05). Both HHcy and folate deficiency were shown to be independent risk factors for UC (95% CI = 1.206-12.293, P = 0.023; 95% CI = 1.910-11.129, P = 0.001, respectively). TCN2 (rs1801198, rs9606756) mutations might aggravate the severity of UC. HHcy and folate deficiency are independent risk factors for UC. [ABSTRACT FROM AUTHOR]