Maternal folic acid intake in the periconceptional period is strongly related to reduction in recurrence and occurrence of birth defects involving the neural tube. Among the single nucleotide polymorphisms (SNPs) influencing the folate metabolism, the methylenetetrahydrofolate reductase (MTHFR) gene has been the one most exclusively studied. Many studies have reported significant association between MTHFR 677C>T and increased risk of neural tube defects (NTDs). Our previous study did not support this observation. The present study aimed to determine the prevalence of 1298A>C polymorphism in addition to 677C>T in the same Turkish population as a risk factor for NTDs. We genotyped case (95 offspring with NTDs, 80 mothers, 72 fathers) and control (93 healthy children) populations for MTHFR 677C>T and MTHFR 1298 A>C polymorphisms. The comparison demonstrated a significant increase in the 1298AA/677TT genotype frequency among mothers of offspring with NTDs (OR 5.23 [1.06-25.9]; p=0.067). The 677CT genotype was only 1.35 times higher than controls among mothers when 677C>T polymorphism was evaluated alone, while 677CT/1298AC in the current study demonstrated a 3.8 times increase in this risk. These observations led us to conclude that although not statistically significant, MTHFR 1298AC polymorphism might be a risk factor for the occurrence of NTDs in the Turkish population.