BACKGROUND: Clinical predictive models leave gaps in our ability to stratify cardiovascular risk. High-throughput molecular profiling promises to improve risk classification. METHODS: Horizon 1 of the Measurement to Understand the Reclassification of Disease of Cabarrus and Kannapolis (MURDOCK) Study was conceived to apply emerging molecular techniques to existing data sets to characterize mechanistic diversity underlying complex human diseases, response to therapy, and prognosis. No previous studies have applied multiple, complementary molecular techniques in combination with well-developed clinical risk models to refine cardiovascular risk prediction. The MURDOCK Cardiovascular Disease Study will assess molecular profiles integrated with clinical data in "clinomic" profiles for cardiovascular risk classification. CONCLUSION: Herein, we describe the design of and rationale for the MURDOCK Cardiovascular Disease Study.