Meta-analyses have reported a 2- to 3-fold increased risk of venous thrombosis (VT) in individuals with hyperhomocysteinemia. However, confounding factors were generally not considered. In contrast, randomized trials of homocysteine-lowering therapy and VT risk have been negative. We investigated whether hyperhomocysteinemia was associated with VT in the Multiple Environmental and Genetic Assessment of Risk Factors for Venous Thrombosis (MEGA) case-control study (1999-2004) from the Netherlands (1,689 cases and 1,726 controls), taking into account measured and unmeasured confounders. We compared patients with population controls to estimate odds ratios using unconditional logistic regression and adjusted for various potential confounders. We matched patients to their partners to additionally adjust for unmeasured confounders (e.g., lifestyle factors) using conditional logistic regression. We found that elevated homocysteine concentrations were not associated with an increased risk for VT when comparing patients with population controls, either as a continuous variable (odds ratio = 1.00, 95% confidence interval: 0.99, 1.01), in terms of 0.7-mg/L increase (odds ratio = 0.99, 95% confidence interval: 0.93, 1.05), or within different homocysteine categories. We obtained similar results when patients were compared with their partners. Stratification by sex, deep vein thrombosis, pulmonary embolism, provoked VT, and unprovoked VT also provided no evidence of an association. In conclusion, after extensive adjustments for confounding, hyperhomocysteinemia was not associated with an increased risk of venous thrombosis in this study.