Little is known about military sexual trauma (MST) in transgender veterans. To address this gap, we examined archival data regarding transgender veterans from the Iraq and Afghanistan conflicts. There were 332 transgender veterans treated at the Veterans Health Administration between 2000 and 2013 (78 men, 254 women; mean age 33.86 years), with most being non-Hispanic White. Transgender status and mental health conditions were identified using the International Classification of Diseases, 9th Revision (ICD-9; World Health Organization, 1980) codes and chart review. Men and women were analyzed separately, using contingency tables and χ2 testing for categorical variables and t tests for continuous variables. Likelihood of having a mental health condition and MST were examined using logistic regression. Among the 15% of participants who experienced MST, MST was associated with the likelihood of posttraumatic stress disorder, adjusted OR = 6.09, 95% confidence interval (CI) [1.22, 30.44] and personality disorder, OR = 3.86, 95% CI [1.05, 14.22] for men and with depressive, OR = 3.33, 95% CI [1.12, 9.93], bipolar, OR = 2.87, 95% CI [1.12, 7.44], posttraumatic stress, OR = 2.42, [1.11, 5.24], and personality disorder, OR = 4.61, 95% CI [2.02, 10.52] for women. Implications include that medical forms should include gender identity and biological gender and that MST treatment should be culturally competent.