Peroxisome proliferator-activated receptor (PPAR) is a nuclear receptor with manifold effects on intermediary metabolism. To define a set of urinary biomarkers that could be employed to determine the efficacy of PPAR agonists, a metabolomic investigation was undertaken in wild-type and Ppar-null mice fed for 2 weeks either a regular diet or a diet containing the PPAR ligand Wy-14,643 and their urine analyzed by ultra-performance liquid chromatography coupled with time of flight mass spectrometry. Principal components analysis of 6393 accurate mass positive ions revealed clustering as a single phenotype of the treated and untreated Ppar (-/-) mice plus two further discrete phenotypes for the treated and untreated Ppar (+/+) mice. Biomarkers of PPAR activation were identified from their accurate masses and confirmed by tandem mass spectrometry of authentic compounds. Biomarkers were quantitated from raw chromatographic data using appropriate calibration curves. PPAR urinary biomarkers highly statistically significantly elevated by Wy-14,643 treatment included 11-hydroxy-3,20-dioxopregn-4-en-21-oic acid (>3,700-fold), 11,20-dihydroxy-3-oxopregn-4-en-21-oic acid (50-fold), nicotinamide (>2-fold), nicotinamide 1-oxide (5-fold), 1-methylnicotinamide (1.5-fold), hippuric acid (2-fold), and 2,8-dihydroxyquinoline--D-glucuronide (3-fold). PPAR urinary biomarkers highly statistically significantly attenuated by Wy-14,643 treatment included xanthurenic acid (1.3-fold), hexanoylglycine (20-fold), phenylpropionylglycine (4-fold), and cinnamoylglycine (9-fold). These biomarkers arise from PPAR effects on tryptophan, corticosterone and fatty acid metabolism and on glucuronidation. This study underscores the power of mass spectrometry-based metabolomics combined with genetically-modified mice in the definition of monogenic metabolic phenotypes.