The mitochondrial myopathies (MM) are a heterogenous group of neuromuscular diseases associated with abnormal mitochondria and defects in mitochondrial oxidative phosphorylation (OXPHOS). Analysis of a broad spectrum of MM patients has revealed that patients with similar clinical symptoms frequently do not have the same muscle OXPHOS defect. To determine whether some of this variation was due to methodological differences between studies, we have made a detailed survey of OXPHOS enzyme analysis procedures. The coupled OXPHOS assays for Complexes I + III and II + III were found to be variable due to competing reactions and complicated interactions between complexes. These problems were resolved by utilizing specific Complex I and III assays. The muscle mitochondria isolated from surgery patients under general anesthesia and prepared by proteinase digestion were observed to give low and highly variable OXPHOS activities. Mitochondria isolated from muscle biopsies performed under local anesthesia and finely sliced prior to homogenization gave higher and more consistent OXPHOS activities. Assays for Complexes I, III and V required mitochondrial sonication to express maximal activity, but Complex IV was prone to inactivation by excessive mechanical disruption. Mitochondria isolated from frozen muscle or from patients with an OXPHOS disease are more fragile than those isolated from fresh tissue and normal individuals. Hence, Complex IV activity can be preferentially lost from frozen and sonicated myopathy patient samples. These results suggest that variation in muscle OXPHOS analysis techniques may account for some of the discrepancies between clinical manifestations and OXPHOS defects and suggest that no single protocol is sufficient to adequately define the OXPHOS defect in MM patients.