Background Coronary artery disease (CAD) is the leading cause of death in the United States, with obesity as a leading preventable risk factor for CAD. Certain biochemical markers have demonstrated strong prediction for cardiovascular events. We hypothesized that in addition to weight reduction, gastric bypass will also induce a salutary effect on the biochemical cardiac risk factors. Methods At a single academic institution, from 2003 to 2004, we measured the biochemical cardiac risk factors in gastric bypass patients preoperatively and at 3, 6, and 12 months postoperatively. These risk factors included total cholesterol, high-density lipoprotein (HDL) cholesterol, low-density lipoprotein cholesterol, total cholesterol/HDL cholesterol ratio, triglyceride/HDL cholesterol ratio, triglycerides, lipoprotein A, high-sensitivity C-reactive protein, and homocysteine. The data were analyzed using the Wilcoxon signed rank test. Results The mean age of the 356 patients was 43 years; 84% were women; the mean body mass index was 47 kg/m 2; 33% were diabetic; 50% were hypertensive; 23% were taking lipid-lowering medications; and 2% had known CAD. Significant improvement occurred in the biochemical cardiac factors from preoperatively to 12 months. The beneficial changes were as follows: total cholesterol, 192 mg/dL preoperatively to 166 mg/dL at 12 months; HDL cholesterol, 46 mg/dL preoperatively to 54 mg/dL at 12 months; low-density lipoprotein, 125 mg/dL preoperatively to 88 mg/dL at 12 months; total cholesterol/HDL cholesterol ratio, 4 preoperatively to 3 at 12 months; triglyceride/HDL cholesterol ratio, 3 preoperatively to 2 at 12 months; triglycerides, 133 mg/dL preoperatively to 92 mg/dL at 12 months; lipoprotein A, 14 mg/dL preoperatively to 13 mg/dL at 12 months; high-sensitivity C-reactive protein, 8 mg/L preoperatively to 1 mg/L; and homocysteine, 10 μmol/L preoperatively to 8 μmol/L at 12 months. Conclusions The results of our study have shown that gastric bypass significantly improves all biochemical markers of CAD risk, particularly C-reactive protein, which had an 80% reduction. As a result, gastric bypass decreases the cardiac risk by both weight loss and advantageous alterations of biochemical cardiac risk factors.