As the burden of infectious disease has decreased, chronic disease has become a major concern in the United States. Although overall, chronic diseases have impacted all demographic groups, race/ethnic groups are not equally affected by these diseases. The unequal difference in such health outcomes is termed health disparities. Health disparities not only negatively impact the affected group, they have the potential to negatively impact the community as a whole. The purpose of this cross-sectional population study was to determine if race/ethnicity would explain the variability in coronary heart disease and overall cancer mortality rates in San Diego County. The six San Diego County Health and Human Services Agency's geographic service areas by race/ethnicity (White, Black, Hispanic, and Asian) and corresponding coronary heart disease and overall cancer mortality rates were included in analysis. Associated factors such as socioeconomic status, gender, age, geography, and behavioral risk factors were included in the analysis. The mean rate of coronary heart disease deaths for the county was 193.08 per 100,000 residents, while the mean rate of overall cancer deaths was 141.88 per 100,000 residents. For coronary heart disease, only race/ethnicity, gender, and age were significantly associated with mortality rates. However, for overall cancer, only race/ethnicity was significantly associated with mortality rate. The results of this study hint at a racial/ethnic health disparity with coronary heart disease and overall cancer mortality. Although further studies will be needed to confirm these results, this study will help local county public health professionals develop tailored prevention measures and intervention programs to decrease the burden of chronic disease in San Diego County.