Systemic sclerosis (SSc) is connective tissue disorder in which fibrosis of the skin and internal organs is the main hallmark. Despite the difficulties of studying a complex disease, significant advances have been achieved in the SSc genetics field. In this review, we will describe the firmest genetic susceptibility markers known to date. We will analyze the most recent findings in the HLA region and in non-HLA genes. Furthermore, we will propose functional connections of these loci with the mechanisms involved in SSc pathogenesis. However, only non-HLA genetic regions that have been associated with SSc at the genome-wide significance level or that have been reported to be associated with the disease in at least two different independent studies will be considered. In spite of the increasing number of SSc genetic susceptibility factors identified, further studies with larger sample sizes, deeper phenotype characterization of the patients and innovative analyses will be needed to translate SSc genetics into clinical practice and patient care in the future.