Autophagy is an intracellular process of macromolecule and organelle degradation, which plays an important role both in maintaining homeostasis and in responding to various harmful stimuli. Recent studies clearly indicate upregulation of autophagy in neurons challenged with brain ischemia. In this paper we present biosynthesis of autophagosomes as well as the role and molecular mechanisms of basal and induced neuronal autophagy. We have also reviewed recently published papers concerning the potential role of autophagy in brain ischemia. Results of both in vivo and in vitro experimental studies indicate that signaling pathways related to autophagy might become a target of new neuroprotective strategies.