The thalamus is known to play a key role in arousal regulation and support of human consciousness. Neuropathological studies have identified thalamic damage as one of the most common abnormalities present in the brains of patients who were in a vegetative state (VS) or a minimally-conscious state (MCS) state at the time of their deaths. Nonetheless, no in vivo studies of thalamic abnormalities in these patients have been conducted. Using high-resolution T1-weighted magnetic resonance images and a novel approach to shape analysis, we investigated thalamic global and regional changes in a sample of patients in a VS or an MCS. Group comparisons and correlations with clinical variables were performed for the total thalamic volume and for each surface vertex. Total thalamic volume was significantly lower in patients than in healthy volunteers. Shape analysis revealed significant bilateral regional atrophy in the dorso-medial body in patients compared to controls; this atrophy was more widespread in VS than in MCS patients. Lower thalamic volume was significantly correlated with worse Disability Rating Scale scores. Shape analysis suggested that the dorso-medial nucleus and the internal medullar lamina were the main regions responsible for this correlation. Our findings suggest that MCS and VS patients present different patterns of regional thalamic abnormalities, and that these differences partially explain their clinical profile.