To characterize gender differences in the prevalence of mental and physical health conditions and evaluate the moderating effect of assaultive trauma on risk for these conditions in a nationally representative sample of male and female U.S. veterans. Cross-sectional data were analyzed from 3157 U.S. veterans from the National Health and Resilience in Veterans Study. Multivariable logistic regression analyses assessed gender differences in health outcomes and evaluated physical and sexual trauma as possible moderators of these outcomes. Compared to male veterans, female veterans had higher prevalence estimates of lifetime posttraumatic stress (OR=3.33) and lifetime and current major depressive (ORs=2.10 and 2.76, respectively) disorders, and lifetime histories of arthritis, migraine headaches, and osteoporosis (ORs ranging 2.14–9.74), but lower prevalence estimates of lifetime nicotine dependence (OR=0.46), lifetime and current alcohol use (ORs=0.19 and 0.36, respectively) and lifetime drug use (OR=0.39) disorders, and lifetime histories of diabetes, heart attack, and high blood pressure (ORs ranging 0.05–0.49). The elevation in risk associated with physical and sexual assault was greater for males than females for numerous health conditions (but greater for females for posttraumatic stress disorder). Results provide a comprehensive assessment and characterization of gender differences in mental and physical health conditions and risk conferred by assaultive trauma for certain conditions in U.S. veterans. •We found substantial gender differences in the prevalence of many health conditions.•Gender differences found are consistent with findings from the general population.•Associations differed by gender and type of trauma on risk for many conditions•Male veterans with sexual assault histories were at increased risk for current MDD.