In this work, to better understand the regulation of autophagy in cystinosis, we analyze macroautophagic flux and chaperone-mediated autophagy using Ctns−/− mice, Ctns−/−-GFP-LC3 transgenic mice and Ctns−/−-derived neonatal skin fibroblasts. The gene discussed is MAP1LC3A; the disease is cystinosis.