Objective: To evaluate the utility of targeted exome sequencing for the molecular diagnosis of mitochondrial disorders, which exhibit marked phenotypic and genetic heterogeneity. Methods:We considered a diverse set of 102 patients with suspected mitochondrial disorders based on clinical, biochemical, and/or molecular findings, and whose disease ranged from mild to severe, with varying age at onset. We sequenced the mitochondrial genome (mtDNA) and the exons of 1,598 nuclear-encoded genes implicated in mitochondrial biology, mitochondrial disease, or monogenic disorders with phenotypic overlap. We prioritized variants likely to underlie disease and established molecular diagnoses in accordance with current clinical genetic guidelines.Results: Targeted exome sequencing yielded molecular diagnoses in established disease loci in 22% of cases, including 17 of 18 (94%) with prior molecular diagnoses and 5 of 84 (6%) without. The 5 new diagnoses implicated 2 genes associated with canonical mitochondrial disorders (NDUFV1, POLG2), and 3 genes known to underlie other neurologic disorders (DPYD, KARS, WFS1), underscoring the phenotypic and biochemical overlap with other inborn errors. We prioritized variants in an additional 26 patients, including recessive, X-linked, and mtDNA variants that were enriched 2-fold over background and await further support of pathogenicity. In one case, we modeled patient mutations in yeast to provide evidence that recessive mutations in ATP5A1 can underlie combined respiratory chain deficiency. Conclusion:The results demonstrate that targeted exome sequencing is an effective alternative to the sequential testing of mtDNA and individual nuclear genes as part of the investigation of mitochondrial disease. Our study underscores the ongoing challenge of variant interpretation in the clinical setting. Mitochondrial disorders are a heterogeneous collection of rare disorders caused by mitochondrial dysfunction.1 Multiple organ systems can be affected, with features that can include myopathy, encephalopathy, seizures, lactic acidosis, sensorineural deafness, optic atrophy, diabetes mellitus, liver failure, and ataxia.2 Mitochondrial disorders can be caused by mutations in the nuclear or mitochondrial genomes, and more than 100 genetic loci have been identified to date.3,4 Whereas these disorders may be inherited in a maternal, recessive, X-linked, or dominant manner, many patients have no obvious family history of the disorder.5-7 Because of phenotypic and locus heterogeneity, traditional sequential genetic tests result in molecular diagnoses for only a fraction of patients.8 Limitations in traditional genetic testing have motivated our group and others to develop "next-generation sequencing" (NGS) approaches for molecular diagnosis.