Pulmonary arterial hypertension (PAH) is a devastating complication of systemic sclerosis (SSc). Although there are screening tests for PAH, such as carbon monoxide diffusing capacity and Doppler echocardiography, these tests are far from perfect, patients are still identified late in the course of disease, and the underlying mechanisms of SSc-associated PAH are poorly understood. Understanding the genetic differences between those patients with SSc who do and do not develop PAH may improve our ability to identify and treat patients earlier in the course of disease. To date, only a few candidate gene association studies and one gene expression analysis have investigated the genetics of PAH in SSc. These studies highlight the important opportunities and challenges for exploration of genetics of complex traits. By appreciating the optimal conduct of genetic studies, along with the role of bioinformatics resources such as the International HapMap database, investigators and clinicians will be better equipped to understand the genetics of SSc-associated PAH.