Huntington's disease (HD) is a neurodegenerative disorder characterised by progressive neuronal death in the basal ganglia and cortex. Although increasing evidence supports a pivotal role for mitochondrial dysfunction in the death of patients' neurons, the molecular bases for mitochondrial impairment have not been elucidated. We provide the first evidence of an abnormal activation of Bcl-2/adenovirus E1B 19-kDa interacting protein 3 (BNip3) in cells expressing mutant huntingtin. In the present study we show abnormal accumulation and dimerisation of BNip3 in mitochondria from human HD muscle cells, HD model cell cultures and brain tissues from HD model mice. Importantly, we have demonstrated that BNip3 co-localises with fragmented mitochondria in HD cells and that blocking BNip3 expression and dimerisation restores normal mitochondrial potential and normal mitochondrial morphology in HD cells. Our data shed light on the molecular mechanisms underlying mitochondrial dysfunction in HD and point to BNip3 as a new potential target for neuroprotective therapy in HD.