Macroautophagy/autophagy is a critical protein degradation pathway that preserves cellular and metabolic homeostasis [1]. It is therefore no surprise that its dysfunction is associated with many human pathologies, impacting directly cellular fate. Although much is known about the molecular machinery that governs the autophagy pathway, how to best monitor autophagy and how to precisely quantify its activity has remained more challenging. This is, at least in part, due to the highly dynamic rearrangement of membranes involved in the autophagy process and the degradation of proteinaceous cargo [2]. In this chapter, we highlight the various techniques currently employed to assess autophagy, focusing primarily on correlative light and electron microscopy and super-resolution microscopy. Context will be provided with regards to complimentary approaches. We emphasize the dynamic nature of the autophagy system, which marker proteins to utilize [3–5], and may be most important, how to discern between steady state protein abundance levels, the major autophagy pathway intermediates, their pool sizes and the autophagy activity, or flux. The techniques highlighted range from biochemical approaches such as western blotting to microscopy techniques, including, various fluorescence-based microscopy approaches, super-resolution structured illumination and correlative light and electron microscopy. Section 2 of the chapter will place emphasis on the importance and outcome measures of each technique, whether it reveals the dynamic nature of autophagy or whether it can integrate machinery and cargo measures. By providing examples where autophagy is functional and dysfunctional, the reader will be able to grasp how to best assess the autophagy pathway at basal levels and in diseased states and how to approach scenarios where autophagy activity requires to be offset. Furthermore, you will learn how to use these techniques so that they are well aligned with the given research question, since some techniques are highly labor intensive, and some performed best at single cell level. Finally, this chapter highlights how to discern not only between autophagy activity, but also how to integrate the respective cargo turnover, using a model system of Alzheimer disease.