Thiamine deficiency (TD) produces lesions in the thalamus, mamillary and medial geniculate nuclei, and inferior colliculus. To clarify the pathogenesis of these lesions, we examined the occurrence of hallmarks of apoptosis following TD in rat brain. Histological assessment showed apoptotic cells in the thalamus and medial geniculate nucleus but not in the inferior colliculus. We used terminal deoxynucleotidyl transferase-mediated deoxyuridine (dUPT)-biotin nick-end labelling (TUNEL) and gel electrophoresis to demonstrate that TD is associated with apoptotic cell death. In the thalamus, DNA fragmentation appeared from day 14 of deficiency and preceded the appearance of ataxia. The inferior colliculus and mamillary nucleus were without electrophoretic DNA fragments, and only rare TUNEL-positive labelling was observed. This model shows a rare combination of both apoptosis and necrosis in the same lesioned brain.