Recent years have seen the realization that macroautophagy (which we will call autophagy) is not only important in yeast but is necessary for diverse functions in plants and animals. Importantly, autophagy can have an impact on human pathologies including infectious diseases, cancers, and neurodegenerative conditions. Thus, we need to be able to measure autophagy accurately in order to understand how it can be regulated physiologically and with exogenous agents.