Schizophrenia is associated with alterations in subcortical volumes, cortical thickness and pro-inflammatory cytokines, that may correlate with clinical features. However, analogous work on methamphetamine-induced psychosis is lacking. This study examines subcortical volumes, frontal cortical thickness and pro-inflammatory cytokines in schizophrenia and methamphetamine-induced psychosis.Diagnosis and symptom severity were determined using the Structured Clinical Interview for Axis I Disorders and the Positive and Negative Syndrome Scale, respectively. Structural T1-weighted images were acquired using a 3-Tesla magnetic resonance imaging scanner. Serum peripheral cytokine concentrations were measured using a multiplex bead array.Schizophrenia (n = 36) and methamphetamine-induced psychosis (n = 27) participants showed decreased left amygdala volumes and frontal cortical thickness compared to healthy controls (n = 32). Schizophrenia participants had increased bilateral caudate, putamen, and nucleus accumbens volumes compared to controls, and greater right globus pallidus and nucleus accumbens volumes compared to the methamphetamine-induced psychosis group. No significant differences were found in cytokine levels between groups or associations with neuroimaging measures.The novel discovery of increased globus pallidus and nucleus accumbens volumes in schizophrenia group compared with methamphetamine-induced psychosis group may show important distinctions in the neurobiology between these conditions. Future investigations should employ larger sample sizes, incorporate longitudinal study designs, and integrate magnetic resonance spectroscopy which may show important neurometabolic signatures in these brain regions in methamphetamine-induced psychosis.