Previous work has demonstrated less accurate alignment of cortical structures for patients with schizophrenia than for matched control subjects when using affine registration techniques. Such a mismatch presents a potential confound for functional neuroimaging studies conducting between-group comparisons. Critically, the same issues may be present for subcortical structures. However, to date no study has explicitly investigated alignment precision for major subcortical structures in patients with schizophrenia. Thus, to address this question we used methods previously validated for assessment of cortical alignment precision to examine alignment precision of subcortical structures. In contrasts to our results with cortex, we found that major subcortical structures (i.e. amygdala, caudate, hippocampus, pallidum, putamen and thalamus) showed similar alignment precision for schizophrenia (N=48) and control subjects (N=45) regardless of the template used (other individuals with schizophrenia or healthy controls). Taken together, the present results show that, unlike cortex, alignment for six major subcortical structures is not compromised in patients with schizophrenia and as such is unlikely to confound between-group functional neuroimaging investigations.