Veterans who are discharged from military service due to misconduct are vulnerable to negative health-related outcomes, including homelessness, incarceration, and suicide. We used national data from the Veterans Health Administration for 218,608 veterans of conflicts in Iraq and Afghanistan that took place after the events of September 11, 2001, to compare clinical diagnoses between routinely-discharged (n = 203,174) and misconduct-discharged (n = 15,433) veterans. Misconduct-discharged veterans had significantly higher risk for all mental health conditions (adjusted odds ratio [AOR] range, 2.5-8.0) and several behaviorally linked chronic health conditions (AOR range, 1.2-5.9). Misconduct-discharged veterans have serious and complex health care needs; prevention efforts should focus on behavioral risk factors to prevent the development and exacerbation of chronic health conditions among this vulnerable population.