Autoimmune diseases affect approximately 5% of the population in Western countries, with high female predominance. Family and twins studies have demonstrated that genetic factors are crucial determinants of susceptibility to autoimmune disease, but no specific genes have yet been identified. Recent studies indicate that X chromosome abnormalities, such as monosomy rates and inactivation patterns, occur in a number of female-predominant autoimmune diseases. We will review herein the most recent evidence on the role of the X chromosome in loss of tolerance and discuss its potential implications. Future studies will identify the X chromosome regions containing candidate genes for autoimmune susceptibility.