Histone deacetylase 1 (HDAC1) is a nuclear enzyme involved in transcriptional repression. We report here that cytosolic HDAC1 is detected in damaged axons in brains of human patients with Multiple Sclerosis and of mice with cuprizone-induced demyelination, ex vivo models of demyelination and in cultured neurons exposed to glutamate and TNF-α. Nuclear export of HDAC1 is mediated by the interaction with the nuclear receptor CRM-1 and leads to impaired mitochondrial transport. The formation of complexes between exported HDAC1 and members of the kinesin family of motor proteins hinders the interaction with cargo molecules thereby inhibiting mitochondrial movement and inducing localized beadings. This effect is prevented by inhibiting HDAC1 nuclear export with leptomycin B, treating neurons with pharmacological inhibitors of HDAC activity or silencing HDAC1 but not other HDAC isoforms. Together these data identify nuclear export of HDAC1 as a critical event for impaired mitochondrial transport in damaged neurons.