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Military sexual trauma (MST) is a significant public health issue associated with adverse psychiatric outcomes, including heightened risk for suicide, posttraumatic stress disorder, depression, and substance use disorders. Recently, research has begun exploring gender-linked disparities in mental health outcomes for individuals who experience MST. The current study assessed whether women who screened positive for MST were at disproportionately higher risk for diagnoses of alcohol-use disorder (AUD) or drug-use disorder (DUD) relative to men. Veterans Health Administration (VHA) clinical data were extracted for 435,690 military veterans who separated from the military between 2004 and 2011 and had at least 5 years of follow-up data after their initial VHA visit until the end of fiscal year 2014. Logistic regression models examined the main and interactive effects of gender and screening positively for MST as predictors of AUD and DUD. MST positive screens were associated with increased rates of both AUD and DUD across genders. Although rates of both AUD and DUD were higher among men, the increased rate of diagnosis associated with MST positive screens was proportionally higher for women than men (interaction adjusted odds ratios = 1.43 and 1.17 for AUD and DUD, respectively), indicating the presence of a gender-linked health risk disparity. This disparity was more pronounced for AUD than DUD (p < .01). The current study adds to previous literature documenting increased risk for women exposed to MST. These findings support efforts to reduce the occurrence of MST and continued use of MST screening measures within the VHA.