Dictyostelium provides a well established model system for the study of mitochondrial biology and disease. Mitochondrial dysfunction in Dictyostelium has been generated by knockout of nonessential nuclear genes encoding mitochondrial proteins, by knockout of targeted mitochondrial genes in a subset of the mitochondria, and by knock down of essential nuclear-encoded mitochondrial proteins. The resulting effects on mitochondrial electron transport and membrane potential can be studied by directly measuring the activities, composition, and assembly or stability of individual mitochondrial respiratory complexes and by using fluorescent probes to assay the mitochondrial membrane potential in vivo. Assays for these are described here. The complexities of mammalian developmental biology have obscured the phenotype-genotype relationships in mitochondrial disease and this has inhibited understanding of the underlying cytopathological mechanisms. By contrast, the Dictyostelium model has revealed a characteristic constellation of downstream phenotypic outcomes that, e.g., point to/show common underlying cytopathological mechanisms in mitochondrial disease. These aberrant phenotypes arise from chronic hyperactivity of the energy-sensing protein kinase AMPK and the assay of the most prominent of them is described here.