Atherothrombotic diseases are complex diseases, arising from the interaction between several genetic and environmental factors. Until recently, the genetic basis of complex diseases in general, and of atherothrombosis in particular, were poorly characterized. Progress in DNA analysis techniques and the increasing level of characterization of the variability of the human genome has recently allowed to study comprehensively the association between genetic variants and diseases. To date, more than 400 genome-wide association studies have been conducted, allowing to identify more than 430 genomic regions at which common genetic variants influence the predisposition to complex diseases of great epidemiological relevance. This review article summarizes the progress achieved in the genetic basis of atherothrombotic diseases such as myocardial infarction and ischemic stroke. The advances achieved so far now await for clinical applications.