The aim of this study was to evaluate the association of nutritional (folate, vitamin B12) and genetic (MTHFR, MTR, MTRR, TCN) determinants of homocysteine metabolism and of superoxide dismutase with Crohn's disease (CD). One hundred forty patients with CD were compared with 248 matched healthy controls. Plasma homocysteine levels were higher in CD patients than controls (11.8 vs 10.4 micromol/L, P= 0.0004). Vitamin B12 and folate levels were lower in CD subjects compared to controls (207 vs 255 pmol/L, P= 0.0082, and 8.6 vs 11 nmol/L, P= 0036, respectively). Patients with a personal history of ileal resection, ileitis, or colectomy had significantly lower vitamin B12 levels. In multivariate analysis, vitamin B12 and MTHFR 677 TT carriers were the two significant independent factors of plasma homocysteine >15 micromol/L in CD patients (P= 0.0187 and 0.0048, respectively). The significant association between homocysteine and vitamin B12 levels remained significant only in patients with the highest superoxide dismutase values (P < 0.0001). The MTRR AA genotype was a significant independent predictor of CD risk (odds ratio 3.7, 95% CI 1.218-11.649, P= 0.0213). The level of superoxide dismutase was significantly higher (P= 0.0143) and was correlated with Crohn's Disease Activity Index (CDAI) scores (P for trend = 0.0276) in patients carrying MTRR AA genotype. Vitamin B12 and MTHFR 677 TT genotype are the main determinants of hyperhomocysteinemia in CD patients. The association of MTRR 66A>G polymorphism with oxidant stress and disease activity provides rationale for screening vitamin deficiencies in these patients.