Numerous abnormal metabolites were identified in large amounts in the urine of hypoglycin-treated rats using capillary gas chromatography/mass spectrometry-computer analysis. These metabolites are not detectable in significant amounts in normal rats' urine. Ten of them have not been previously associated with hypoglycin administration: these are several hydroxy compounds, including those from the valine and isoleucine pathways, 2-oxo-adipic acid, n-butyrylglycine and isovaleryl glucuronide. These results indicate that the pathways of isoleucine and valine metabolism are inhibited at their respective acyl-CoA dehydrogenation steps, as is the case for fatty acid, leucine and lysine metabolism, as previously shown. The mass spectra of the trimethylsilyl derivatives of cis, cis-4,7-decadiene-1,10-dioic, cis-4-decene-1,10-dioic, cis-4-octene-1,8-dioic acids, and (methylenecyclopropyl)acetylglycine, which were previously identified using nuclear magnetic resonance and oxidative cleavage or acid hydrolysis, are presented for the first time.