Urinary organic acid analysis is a vital diagnostic tool in the investigation of patients with suspected inborn errors of metabolism. Recent descriptions of diseases producing abnormal chiral metabolites have provided the need for individual enantiomer analysis. In this paper the isolation and simultaneous stereodifferentiation of lactic, glyceric and 2-hydroxyglutaric acids using capillary gas chromatography on heptakis (2,3-di-O-methyl-6-O-tert.butyldimethylsilyl)-beta-cyclodextrin as the chiral stationary phase is described. The diagnostic potential of this method is demonstrated by the analysis of urine samples from two patients with D-2-hydroxyglutaric aciduria and a dog with D-glyceric aciduria. Due to the lack of specific clinical symptoms in these diseases, enantiomeric analysis is vital for diagnosis enabling prompt therapeutic intervention.