Research in chronic alcoholics on memory, decision-making, learning, stress, and reward circuitry has increasingly highlighted the importance of subcortical brain structures. In addition, epidemiological studies have established the pervasiveness of co-occurring psychiatric diagnoses in alcoholism. Subcortical structures have been implicated in externalizing pathology, including alcohol dependence, and in dysregulated stress and reward circuitry in anxiety and mood disorders and alcohol dependence. Most studies have focused on active or recently detoxified alcoholics, while subcortical structures in long-term abstinent alcoholics (LTAA) have remained relatively uninvestigated. Structural MRI was used to compare volumes of 8 subcortical structures (lateral ventricles, thalamus, caudate, putamen, pallidum, hippocampus, amygdala, and nucleus accumbens) in 24 female and 28 male LTAA (mean abstinence=6.3 years, mean age= 46.6 years) and 23 female and 25 male nonalcoholic controls (NAC) (mean age=45.6 years) to explore relations between subcortical brain volumes and alcohol use measures in LTAA and relations between subcortical volumes and psychiatric diagnoses and symptom counts in LTAA and NAC. We found minimal differences between LTAA and NAC in subcortical volumes. However, in LTAA, but not NAC, volumes of targeted subcortical structures were smaller in individuals with versus without comorbid lifetime or current psychiatric diagnoses, independent of lifetime alcohol consumption. Our finding of minimal differences in subcortical volumes between LTAA and NAC is consistent with LTAA never having had volume deficits in these regions. However, given that imaging studies have frequently reported smaller subcortical volumes in active and recently detoxified alcoholics compared to controls, our results are also consistent with the recovery of subcortical volumes with sustained abstinence. The finding of persistent smaller subcortical volumes in LTAA, but not NAC, with comorbid psychiatric diagnoses, suggests that the smaller volumes are a result of the combined effects of chronic alcohol dependence and psychiatric morbidity and suggests that a comorbid psychiatric disorder (even if not current) interferes with the recovery of subcortical volumes.