This paper describes the characterization of glucuronide and sulfuric acid conjugates and alkyl phosphates by thermospray tandem mass spectrometry (MS/MS). Primary thermospray mass spectra were generated using ammonium acetate buffer and filament-on ionization with both positive and negative ion detection. In positive ion mode molecular weight information was obtained for glucuronic, phosphoric and other weak acids. Under these conditions, however, spectra were not obtained for the sulfate adducts or phosphate salts. Negative ion thermospray mass spectrometry was more versatile, providing spectra of all metabolic structures examined. Positive and negative ion mass spectra provided complementary information for glucuronic acids. Collisionally activated dissociation (CAD) mass spectra of the glucuronide [M + NH4]+ or [M - H]- ions exhibited characteristic glucuronide 'fingerprints' as well as prominent aglycone ions. The aryl sulfates were hydrolyzed to the corresponding phenols under buffer/thermospray conditions and for these analytes CAD mass spectra were obtained from [phenate]- or [phenol + acetate]- parent ions. The M- of dimethyl thiophosphate underwent sequential loss of alkyl and alkoxy radicals and formaldehyde with collisional activation. MS/MS greatly enhances the power of the thermospray interface by providing fragmentation information useful both in the identification of unknowns and for improved mass spectrometry specificity.