The human thalamus participates in multiple cortical and subcortical circuits and is important for the healthy brain’s function. Structural changes in the thalamus have been reported for multiple neurological and psychiatric disorders. However, most of the existent studies included small samples, covered few brain disorders, or only investigated the whole thalamus, without taking into account the heterogeneity of this structure. Here, we aimed to investigate the volumes of thalamic subregions across several common brain disorders and the healthy population in a multi-site sample. In a large multi-site sample (N > 9000), we segmented 50 nuclei bilaterally on structural brain scans. We included patients covering 11 clinical conditions including mild cognitive impairement, dementia, major depressive disorder, schizophrenia and risk for schizophrenia, bipolar disorder, autism spectrum disorder, attention-deficit and hyperactivity disorder, Parkinson’s disease and multiple sclerosis. We found that some regions of the thalamus were significantly smaller in many of the disorders, including psychiatric and neurological. We also found specific differences between groups when looking at individual nuclei. Our study highlights a role for the thalamus in the expression of common brain disorders, a possible differential involvement of different subregions, in particular those of the higher order thalamus, and its clinical potential.