Sex-related outcome disparities following severe trauma have been demonstrated in human and animal studies however sex hormone status could not fully account for the differences. This study tested whether X-linked cellular mosaicism, which is unique to females, could represent a genetically based mechanism contributing to sex-related immuno-modulation following trauma. Serial blood samples collected for routine laboratory tests were analyzed for ChrX inactivation (XCI) ratios in white blood cells. 39 severely injured (mean ISS 19) female trauma patients on mixed racial and ethnic background were tested for initial (baseline) and trauma-induced changes in XCI-ratios and their associations with severity of injury and clinical outcome. At admission, two third of the patients showed XCI-ratio values between one and three, about a third presented skewed XCI-ratios (3–7 range) and three patients displayed extremely skewed XCI-ratios (8–30 range). Serial blood samples during the clinical course showed additional changes in XCI-ratios ranging between 20–900% over initial. Increasing XCI-ratios during the injury course correlated with the severity of trauma, subsequent need for ventilator support and pneumonia. In contrast, initial XCI-ratios did not show correlations with injury severity or clinical complications. Initial XCI-ratios showed a positive correlation with age but older patients retained the ability to mount trauma-induced secondary XCI changes. These data shows that trauma results in X-linked cell selection in females, which is likely to be driven by polymorphic differences between the parental ChrXs. X-linked white blood cell skewing correlates with injury severity and a complicated post-injury clinical course. Female X-linked cellular mosaicism and its capacity to change dynamically during the injury course compared to the lack of this machinery in males may represent a novel immuno-modulatory mechanism contributing to sex-based outcome differences after injury and infection.