Mitochondria play a number of important roles, including production of ATP for the generation of energy, involvement in the regulation of excitotoxicity, involvement in the homeostasis of intracellular Ca2+, production of reactive oxygen species, and the release of cytochrome c, a potent trigger of programmed cell death (apoptosis). Mitochondrial dysfunction has long been implicated in the pathogenesis of neurodegenerative disorders such as Parkinson's disease and amyotrophic lateral sclerosis (ALS), and in physiological conditions such as aging. Mitochondrial dysfunction has also been associated with endoplasmic reticulum (ER) stress caused by the accumulation of misfolded or unfolded proteins due to decreased ER-associated degradation (ERAD), by which misfolded or unfolded proteins are transported from the lumen of the ER to the cytoplasm, where they are ubiquitinated and eventually eliminated. The mitochondria may undergo various morphological alterations reflective of different pathological conditions and diseases. The transmission electron microscope (TEM) remains a powerful tool for the morphological examination of mitochondria and is expected to continue to enhance our understanding of cellular functions and dysfunction. Moreover, electron microscopic study has enabled us to confirm mitochondrial involvement in the pathomechanism of certain neurodegenerative diseases. Here, electron-microscopy procedures are outlined with particular emphasis on some practical aspects of this approach. Electron-micrographs of mitochondrial alterations under various normal and pathological conditions are provided, including images from human control individuals, patients with ALS, and familial ALS-related mutant SOD1 (G93A and H46R) transgenic mice.