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There is considerable concern about the emergence of significant substance abuse among younger veterans of war in the Middle East, especially among those with Posttraumatic Stress Disorder (PTSD), but little information exists on the magnitude of this problem. Using national administrative data from the Department of Veterans Affairs (VA) (n = 1,001,996), we examined rates of diagnosed substance use disorders in Veterans who served in Iraq and Afghanistan diagnosed with PTSD compared to other psychiatric disorders; and compared rates among veterans of other service eras. Of VA patients with a selected mental disorder, 21.0% had a comorbid substance diagnosis. Veterans who served in the post-Vietnam era (VET) (1973–1991) had the highest rates of comorbidity. Logistic regression models indicated that veterans with each selected psychiatric diagnosis were significantly more likely to be dually diagnosed in comparison to veterans with PTSD; post-Vietnam veterans were significantly more likely to be dually diagnosed than veterans from other eras. Bipolar disorder and schizophrenia are most strongly associated with dual diagnosis in OEF/OIF (Operation Enduring Freedom/Operation Iraqi Freedom) veterans. There are high rates of substance use disorders among veterans with mental illness. The highest rates of comorbidity occur among those with bipolar disorder and schizophrenia; and in post-VET veterans. (Am J Addict 2011;00:1–5)