Mitochondrial oxidative phosphorylation (OXPHOS) disorders are a heterogeneous group of diseases with variable expression that often pose diagnostic dilemmas. Although definitive diagnosis of these disorders usually requires a muscle biopsy and mtDNA and enzymatic testing, standard metabolic studies including organic acid and amino acid analysis often provide useful findings that support an OXPHOS disease and the need for more invasive studies. In addition, the detection of possible metabolic derangements, such as elevated lactate levels, may lead to improved long-term outcomes for affected patients through the use of various treatment regimens. Similarly, long-term yearly monitoring of diagnosed OXPHOS patients with metabolic testing is also warranted.