Abstract-Hyperhomocysteinemia, a risk factor for cardiovascular disease, is caused by nutritional or genetic disturbances in homocysteine metabolism. A polymorphism in methylenetetrahydrofolate reductase (MTHFR) is the most common genetic cause of mild hyperhomocysteinemia. To examine mechanisms by which an elevation in plasma homocysteine leads to vascular disease, we first performed microarray analyses in livers of Mthfr-deficient mice and identified differentially expressed genes that are involved in lipid and cholesterol metabolism. Microarrays and RT-PCR showed decreased mRNA for apolipoprotein A (ApoA)-IV and for ApoA-I and increased mRNA for cholesterol 7␣ hydroxylase (Cyp7A1) in Mthfr ϩ/Ϫ mice compared with Mthfr ϩ/ϩ mice. Western blotting revealed that ApoA-I protein levels in liver and plasma of Mthfr ϩ/Ϫ mice were 52% and 62% of levels in the respective tissues of Mthfr ϩ/ϩ mice. We also performed Western analysis for plasma ApoA-I protein levels in 60 males with coronary artery disease and identified a significant (PϽ0.01) negative correlation (Ϫ0.33) between ApoA-I and plasma homocysteine levels. This cohort also displayed a negative correlation (Ϫ0.24, Pϭ0.06) between high-density lipoprotein cholesterol and plasma homocysteine. Key Words: homocysteine Ⅲ methylenetetrahydrofolate reductase Ⅲ apolipoprotein A-I Ⅲ high-density lipoprotein Ⅲ peroxisome proliferator-activated receptor ␣ C onventional risk factors for cardiovascular disease including hypercholesterolemia, hypertension, smoking, and diabetes account for approximately 50% of all cases. 1 Evidence now indicates that hyperhomocysteinemia (HHcy), which occurs in Ϸ5% to 7% of the general population, is an important risk factor for atherosclerotic and thrombotic disease. 2 The enzyme 5,10-methylenetetrahydrofolate reductase (MTHFR) plays a critical role in regulating total homocysteine (tHcy) levels by synthesizing 5-methyltetrahydrofolate, which provides the methyl group for homocysteine remethylation to methionine. Mild deficiency of MTHFR, the most common genetic cause of mild HHcy, occurs frequently in many populations (10% to 15% of individuals) and is attributable to homozygosity for a polymorphism (677C3 T) that reduces enzyme activity. 3 To generate an animal model for HHcy, we had created mice with a heterozygous (ϩ/Ϫ) disruption of the Mthfr gene. 4 With Ϸ50% residual activity and Ϸ1.7-fold greater levels of plasma tHcy compared with their wild-type (ϩ/ϩ) littermates (5.4Ϯ1.0 versus 3.2Ϯ1.2, meanϮSD), 4 the Mthfr