In order to examine correlations which might be useful in ascertaining or confirming the diagnosis of mitochondrial disease, a retrospective analysis of urine organic acids was performed. Among 3646 analyses from randomly selected samples referred to our laboratory, there were 258 specimens from 67 patients with various known disorders of mitochondrial oxidative function, most of whom were known to have chronic and persistent elevations of blood lactic acid, and 176 samples from 21 patients with diagnosed organic acidemia. Urine lactate was not a useful discriminator; only 7.6% of results from infants with mitochondrial disease fell the 95th percentile for patients without mitochondrial disease. Most of the Krebs cycle intermediates were also not useful in discriminating patients with mitochondrial disorders. Interestingly, there was strikingly poor correlation among most of those analytes in all patient groups, but fumarate and malate were uniquely well correlated (r2 = 0.840). Fumarate and malate were also the most useful in distinguishing patients with mitochondrial disease and organic acidemia from the pool of unselected or undiagnosed patients, although the utility was somewhat limited. Using a cutoff value of approximately 90 mmol/mol creatinine for fumarate or malate at age <1 year, or a cutoff of approximately 25 for older patients, 25ndash; 30% of mitochondrial disease patients can be distinguished with a 5% false positive rate. Further refinements to this approach may better characterize the metabolomic profile and may improve the diagnostic utility of quantitative organic acid analysis in mitochondrial disease.