A hybrid quadrupole orthogonal time-of-flight mass spectrometer (QToF) equipped with a solids analysis probe (atmospheric solids analysis probe-mass spectrometry (ASAP-MS)) has been applied to the high throughput qualitative analysis of bile (rat and dog) and urine (rat) samples. The metabolic profiles generated by ASAP-MS was less comprehensive than that provided by liquid chromatography (LC) or gas chromatography-mass spectrometry (GC-MS) metabonomic profiling, though simple types of sample preparation were found to increase the range of ions detected for bile (a complex, multicompartment sample type). While unsuited to biomarker discovery, ASAP-MS of these biofluids generated sufficiently complex metabolic fingerprints to enable them to be distinguished from each other using multivariate statistical methods such as principal components analysis (PCA). This ability to provide an effective means of sample classification suggests possible diagnostic applications.