Sjögren's syndrome is typified by a strong female predilection which is also observed in other systemic autoimmune diseases. Although many factors may be contributing to this phenomenon, the exact underlying mechanisms remain unclear. Apart from the traditionally considered hormonal and environmental factors, lately the role of sex chromosomes and especially of the X chromosome has drawn much attention. In the current review, we focus on the inherent genetic imbalance between the sex chromosomes and their influence and role on gender-discordant disease presentation. To compensate for this imbalance, nature has created a defective epigenetic mechanism to silence the second rich in immune related genes X chromosome. Genes escaping silencing, transfer the genetic imbalance into the transcriptional and protein level, contributing to gender differences as reflected in functions of the innate and adaptive immunity. Under this prism, recent research data on SS, regarding specific immune X-linked loci are being presented and analysed. The "X Factor" in the search for an explication of women's predilection in autoimmunity, may lie behind these unique properties of the X chromosome.