Aim: To investigate the maternal homocysteine (Hcy), folate, vitamin B12 and B6, and their relations to neural tube defects (NTDs). Methods: Thirty mothers of NTDs offspring and another 60 mothers of normal children were enrolled as the patient and control groups from Xinjiang, China, from January 2008 to May 2011. The plasma levels of Hcy, folate, vitamin B12 and B6 were measured and compared between the two groups. Results: The morbidity of NTDs was 2.44% in Xinjiang. The Hcy was significantly higher in patient group than in control group (15.1 +/- 7.8 vs. 8.5 +/- 4.0 mu mol/L, p < 0.001). The folate in patient group (9.7 +/- 8.1 mu g/L) was lower than in control group (15.0 +/- 8.1 mu g/L, p < 0.001). The vitamin B12 was 181.3 +/- 107.7 and 394.3 +/- 386.3 ng/L in patient and control groups, respectively, with a significant difference (p < 0.001). The abnormal frequency of Hcy and vitamin B12 was statistically different in two groups. The difference of vitamin B6 between the patients and controls was marginal (48.7 +/- 16.5 vs. 42.0 +/- 10.5 mg/L, p = 0.051). Moreover, folate and vitamin B12 levels were negatively correlated with Hcy while vitamin B6 was positively correlated with Hcy. Positive correlation was observed between folate and vitamin B12 levels. Conclusion: Our data confirm that higher Hcy, lower folate and vitamin B12 are risk factors for NTDs. Besides folate, vitamin B12 should be supplied to decrease NTDs occurrence. Further study is required to investigate the levels and accurate role of vitamin B6.