Keywords: neurodegeneration, neuronal death, acute brain damage, rapamycin, neuroprotectionAbbreviations: ANOVA, analysis of variance; APs, autophagosomes; Becn1, beclin 1; CNS, central nervous system; Cyt-c, cytochrome-c; CQ, chloroquine; GFP, green fluorescent protein; HCb, hemicerebellectomy; IO, inferior olive; LC3, microtubule-associated protein 1 light chain 3; mTOR, mammalian target of rapamycin; NeuN, neuron specific nuclear protein; NSS, neurological severity score; Pn, pontine nuclei; Rap, rapamycin; Sal, saline Autophagy is the evolutionarily conserved degradation and recycling of cellular constituents. In mammals, autophagy is implicated in the pathogenesis of many neurodegenerative diseases. However, its involvement in acute brain damage is unknown. This study addresses the function of autophagy in neurodegeneration that has been induced by acute focal cerebellar lesions. We provide morphological, ultrastructural, and biochemical evidence that lesions in a cerebellar hemisphere activate autophagy in axotomized precerebellar neurons. Through time course analyses of the apoptotic cascade, we determined mitochondrial dysfunction to be the early trigger of degeneration. Further, the stimulation of autophagy by rapamycin and the employment of mice with impaired autophagic responses allowed us to demonstrate that autophagy protects from damage promoting functional recovery. These findings have therapeutic significance, demonstrating the potential of pro-autophagy treatments for acute brain pathologies, such as stroke and brain trauma.