The purpose of this study was to describe differences in cardiovascular risk factor prevalences and clustering patterns among the states and federal territories of Malaysia. Risk factors considered were abdominal obesity, diabetes, hypertension, hypercholesterolemia and smoking. Using data from the third National Health and Morbidity Survey (NMHS III) in 2006, we estimated the states and federal territories risk factor prevalences and clustering patterns to map the cardiovascular burden distribution in Malaysia. There was a clear geographical variation in the distribution of the individual risk factors as well as in its clustering with remarkable impact seen in Peninsular Malaysia. Perlis, Kedah and Kelantan were the most affected states overall.