Overview of the autophagy pathway, its key molecular players and protocols. The numbered star symbols relate to the accompanying protocols; “EM” refers to electron microscopy (not described), which can detect double-membrane vesicles. Protocols 1 and 2 detect lipidated LC3; Protocol 3 quantifies the fusion of lysosomes with autophagosomes; Protocol 4 detects the presence of nondegraded adaptor protein p62 on tissue sections, an indication of reduced levels of autophagy; and Protocol 5 measures mitochondrial damage, a consequence of reduced autophagy. Abbreviation: PE, phosphatidylethanolamine. (1) Protocol: Monitoring Autophagic Flux by Using Lysosomal Inhibitors and Western Blotting of Endogenous MAP1LC3B (Chittaranjan et al. 2015); (2) Protocol: Monitoring the Localization of MAP1LC3B by Indirect Immunofluorescence (Ktistakis 2015); (3) Protocol: Analyzing the Colocalization of MAP1LC3 and Lysosomal Markers in Primary Cells (Phadwal 2015); (4) Protocol: Detection of p62 on Paraffin Sections by Immunohistochemistry (Watson and Soilleux 2015); (5) Protocol: Detection of Mitochondrial Mass, Damage, and Reactive Oxygen Species by Flow Cytometry (Puleston 2015).