Through the process of oxidative phosphorylation (OXPHOS), mitochondria provide cells with required energy in the form of ATP. The organelle possesses its own genome (mtDNA), which encodes for part of the components needed (37 genes encoding either OXPHOS structural subunits or tRNAs and rRNAs). Nonetheless, the majority of structural OXPHOS components (as well as accessory proteins and proteins required for maintenance, replication, and expression of the mtDNA) are encoded by nuclear genes. Due to the dual genetic control and the large number of proteins involved, biogenesis and assembly of the OXPHOS system is complicated, and identifying a specific gene defect can be a difficult and time consuming task. This unit describes procedures for obtaining tissue sections and cell material suitable for histological evaluation of OXPHOS activity and integrity and immunodetection of the complexes in tissue from patients suspected of mitochondrial disease. Emphasis lies on the diagnostic potential of these techniques to differentiate mtDNA from nuclear mutations. Curr. Protoc. Hum. Genet. 63:19.2.1‐19.2.19. © 2009 by John Wiley & Sons, Inc.