AbstractAutophagy has been shown to be activated in neuronal cells in response to injury and suggested to have a cell‐protective role in neurodegenerative diseases. In this study, we investigated the activation of autophagy in retinal ganglion cells (RGCs) following optic nerve transection (ONT) and evaluated its effect on RGC survival. Expression of several autophagy‐related genes, including Atg5, Atg7, and Atg12, and autophagy markers microtubule‐associated protein 1 light chain 3–II (LC3‐II) and beclin‐1 were analyzed at the transcriptional or protein level 1, 3, and 7 days after ONT. Transcription of the Atg5, Atg7, and Atg12 genes was up‐regulated 1.5‐ to 1.8‐fold in the retina 3 days after ONT compared with that in the controls. Expression of Atg12 mRNA was increased 1.6‐fold 1 day after ONT. Seven days after ONT, expression of Atg5, Atg7, and Atg12 mRNA was comparable to that in the untreated retinas. Western blot analysis of proteins isolated from RGCs showed 1.6‐, 2.7‐, and 1.7‐fold increases in LC3‐II level 1, 3, and 7 days after ONT, respectively, compared with those in the controls. Expression of beclin‐1 was 1.7‐fold higher 1 day after RGCs were axotomized, but 3 and 7 days after ONT it was comparable to that of the control. Inhibition of autophagy with bafilomycin A1, 3‐methyladenine, and Wortmannin in RGC‐5 cells under serum‐deprived conditions decreased cell viability by approximately 40%. These results suggest possible activation of autophagy in RGCs after optic nerve transection and demonstrate its protective role in RGC‐5 cells maintained under conditions of serum deprivation. © 2008 Wiley‐Liss, Inc.