This chapter describes detailed methods to monitor autophagy in neurodegenerative disorders, especially in Alzheimer's disease. Strategies to assess the competence of autophagy-related mechanisms in disease states ideally incorporate analyses of human disease and control tissues, which may include brain, fibroblasts, or other peripheral cells, in addition to animal and cell models of the neurodegenerative disease pathology and pathobiology. Cross-validation of pathophysiological mechanisms in the diseased tissues is always critical. Because of the cellular heterogeneity of the brain and the differential vulnerability of the neural cells in a given disease state, analyses focus on regional comparisons of affected and unaffected regions or cell populations within a particular brain region and include ultrastructural, immunological, and cell and molecular biological approaches.