Electron microscopy (EM) is a reliable method for diagnosing mitochondrial diseases in striated muscle biopsy in infancy. Ultrastructural alterations in mitochondria of myofibers are well documented, but there are few studies of endothelial involvement in intramuscular capillaries. Quadriceps femoris biopsies of five representative infants and toddlers, ages neonate to 3.5 years, were performed because of clinical and laboratory data consistent with mitochondrial disease without mitochondrial DNA (mtDNA) mutations and likely with nuclear DNA mutations. Pathological studies included histochemistry, EM, respiratory chain enzymatic assay and mtDNA sequencing and deletion/duplication analysis. EM demonstrated frequent and severe alterations of mitochondria in capillary endothelium. The most constant changes included: either too few or fragmented cristae; stacked and whorled cristae; paracrystallin structures that often were large and spheroid with stress fractures; closely apposed membranes of granular endoplasmic reticulum surrounding mitochondria with loss of the normal intervening layer of cytoplasm; long narrow, thin looped microvilli extending into the lumen; and thick microvilli containing large, abnormal mitochondria. We conclude that mitochondrial cytopathies in early life exhibit more severe ultrastructural alterations in the endothelium than in myofibers and that paracrystallin body structure differs, perhaps due to less rigid surrounding structures. This distribution may explain the frequent lack of prominent histochemical and biochemical abnormalities in muscle biopsies of young patients. Endothelial changes do not distinguish the genetic defects. Vascular involvement in brain contributes to cerebral lesions and neuronal death by impairment of molecular and nutrient transport and ischemia; endothelium in muscle may reflect similar changes.