The pig is a recognized model for the onset of coronary heart disease and heart attacks. Previous studies have shown that serum cholesterol levels in the pig can be elevated using a high fat, high cholesterol (HFHC) diet. What has been lacking is a genetically defined model corresponding to human ApoE4 susceptibility that can be linked to diets capable of inducing atherosclerosis. This study used a cloned pig model to examine the impact of cholesterol levels with the development of aorta fatty deposits leading to atherosclerosis. Diets were formulated using vegetable sources of protein to provide similar intakes of metabolizable energy, calcium, phosphorous and principal amino acids in both control and HFHC groups. After 60 days, the HFHC group demonstrated a 40-fold increase in aortic fatty streak lesion area combined with 6- and 11-fold increases in total and LDL cholesterol, respectively, over control diet fed cloned pigs. Previous studies have suffered from either imbalanced total caloric intake, an overall imbalance in the nutrition of the control versus HFHC groups or genetic heterogeneity when evaluating dietary constraints related to atherosclerosis. This study demonstrated that cloned, genetically-defined ApoE4 pigs provided balanced nutrition diets provide an experimental system ideally suited to examining atherosclerosis and the onset of coronary heart disease.