BACKGROUND Disorders within the schizophrenia spectrum genetically overlap with bipolar disorder, yet questions remain about shared biological phenotypes. Investigation of brain structure in disease has been enhanced by developments in shape analysis methods that can identify subtle regional surface deformations. Our study aimed to identify brain structure surface deformations that were common across related psychiatric disorders, and characterize differences. METHODS Using the automated FreeSurfer-initiated Large Deformation Diffeomorphic Metric Mapping, we examined volumes and shapes of seven brain structures: hippocampus, amygdala, caudate, nucleus accumbens, putamen, globus pallidus and thalamus. We compared findings in controls (CON; n = 40), and those with schizophrenia (SCZ; n = 52), schizotypal personality disorder (STP; n = 12), psychotic bipolar disorder (P-BP; n = 49) and nonpsychotic bipolar disorder (N-BP; n = 24), aged 15-35. Relationships between morphometric measures and positive, disorganized and negative symptoms were also investigated. RESULTS Inward deformation was present in the posterior thalamus in SCZ, P-BP and N-BP; and in the subiculum of the hippocampus in SCZ and STP. Most brain structures however showed unique shape deformations across groups. Correcting for intracranial size resulted in volumetric group differences for caudate (p < 0.001), putamen (p < 0.01) and globus pallidus (p < 0.001). Shape analysis showed dispersed patterns of expansion on the basal ganglia in SCZ. Significant clinical relationships with hippocampal, amygdalar and thalamic volumes were observed. CONCLUSIONS Few similarities in surface deformation patterns were seen across groups, which may reflect differing neuropathologies. Posterior thalamic contraction in SCZ and BP suggest common genetic or environmental antecedents. Surface deformities in SCZ basal ganglia may have been due to antipsychotic drug effects.