Muscle histology is an essential component of the diagnostic work-up for mitochondrial cytopathies and is very important in both ruling in disease as well as ruling out the disease (i.e., alternate diagnoses). A muscle biopsy method must provide tissue for histology, electron microscopy, enzymes and DNA and this can be obtained with a suction-modified 5 mm needle. Proper embedding and processing is important for optimal diagnostic yield. The essential stains for mitochondrial histology remain the modified Gomori trichrome, cytochrome oxidase, succinate dehydrogenase, and NADH. Electron microscopy can be helpful in selected cases, however, the decision to perform this on all samples remains a contentious issue. Some cases of mitochondrial cytopathy may show no abnormalities on histology or electron microscopy (i.e., LHON), whereas, other conditions can mimic mitochondrial disease through secondary mitochondrial changes (i.e., inclusion body myositis). Athletes show evidence of increased mitochondrial numbers but do not normally develop ragged red fibers or paracrystalline inclusions. Aging is associated with an accumulation of mitochondrial abnormalities and is an important factor to consider in the interpretation of the sample. For example, biopsies in young children with mitochondrial disease may be normal at the histological level and otherwise healthy older adults can show mitochondrial changes such as ragged red and COX-negative fibers.