Elevated levels of homocysteine, an intermediary product of the methionine metabolism, are an established risk factor for atherosclerosis and arterial thrombosis. Hyperhomocysteinemia ultimately leads to endothelial dysfunction with associated platelet activation and thrombus formation. Mild to moderate forms can be caused by homozygosity for a common 677C>T point mutation in the coding region of the MTHFR gene. The second common MTHFR mutation 1298A>C also contributes to reduced enzyme activity, especially when occurring simultaneously with 677C>T. Fasting homocysteine levels are significantly higher in individuals heterozygous for both substitutions compared with individuals carrying only the heterozygous 677C>T mutation. Hyperhomocysteinemia may affect methotrexate sensitivity and contribute to toxicity, as MTHFR is an important enzyme in maintaining cellular folate pools. Thus, homozygosity for 677C>T or compound heterozygosity for 677C>T/1298A>C conveys a significantly higher risk for negative side-effects of methotrexate medication.