Autoimmune diseases altogether affect approximately 5% of the population in Western countries, with a higher prevalence in women. Exploring the biological differences between sexes, great attention was focused on hormones and, more recently, on fetal microchimerism, without reaching definitive evidence. Genetic factors are known to be crucial determinants of susceptibility, as shown by family and twin studies, although no specific genes predisposing women to autoimmunity have been identified thus far. In this article, we review recent data regarding X-chromosome abnormalities, such as inactivation patterns and X monosomy, that characterize some female-predominant autoimmune diseases. We believe that future high-throughput tools will help to identify specific clusters of genes on the sex chromosomes that are candidates for disease susceptibility or resistance.