People with higher general cognitive ability in early life have more favourable levels of cardiovascular disease (CVD) risk factors in adulthood and CVD itself. The mechanism of these associations is not known. Here we examine whether general cognitive ability and CVD risk factors share genetic and/or environmental aetiology. In this large, pedigree-based cross-sectional study of Scottish families ( N = 1983 families; 6086 individuals) we estimate the heritability (ranging from 0.08 to 0.91) of a diverse battery of CVD risk factors, and also examine the extent and causes of their relationship with general cognitive ability. General cognitive ability was associated significantly with almost all the risk factors investigated, explaining between 0.2% and 11% of variance. For those measures with an effect size greater than around 1%, the relationship was primarily influenced by genes (30 to 94%) rather than the environment. These findings have relevance to the growing field of cognitive epidemiology, in which intelligence is used to predict morbidity and mortality. We provide evidence that risk factors such as education and income – which are typically treated as environmental indicators by epidemiologists and controlled for in their studies of morbidity – are genetically confounded with IQ.