Early identification of cardiovascular diseases allows us to prevent the progression of these diseases. The Bale/Doneen Method, a prevention and treatment program for heart attacks and ischemic strokes, has been adopted nationally in primary care and specialty clinics. The main purpose of this study was to evaluate the effect of the Bale/Doneen Method on lipoproteins and carotid intima-media thickness (IMT) for cardiovascular disease prevention and reduction. A secondary purpose was to illustrate the use of latent growth-curve analysis in studying trajectories of clinical outcomes and biomarkers in individual patients over time. This retrospective analysis is based on 576 patients at a nurse-managed ambulatory clinic who received the heart attack prevention and treatment program from 2000 to 2008. All patients were white; 61% were men; mean age was 55.5 years. Outcome measures include hemoglobin A1c, fasting blood sugar, plaque burden score (PBS), high-density lipoprotein, low-density lipoprotein (LDL), mean carotid artery IMT, and lipoprotein-associated phospholipase A2 test results. Latent growth-curve analysis was used in modeling changes in these outcome measures. On average, mean IMT score decreased by 0.01 per year (P < .001), PBS decreased by 0.17 per year (P < .001), LDL decreased by 5.19 per year (P < .001), and lipoprotein-associated phospholipase A2 decreased by 3.6 per year (P < .05). Hemoglobin A1c increased by 0.04 per year (P < .001). Significant sex and age differences in the initial level and/or rate of change of mean IMT, PBS, fasting blood sugar, high-density lipoprotein, and LDL scores were found. The current findings suggest that the Bale/Doneen Method is effective in generating a positive effect on the atherosclerotic disease process by achieving regression of disease in the carotid arteries.