In this paper we report about the biodegradation of the beta-blocker atenolol and the hypoglycaemic agent glibenclamide. The biodegradation tests were performed in batch reactors under aerobic conditions, using as inocculums sewage sludge from a conventional activated sludge treatment and a laboratory-scale membrane bioreactor. Pharmaceuticals were used as sole carbon sources, spiked at 50ng/L and 10mg/L concentrations. Quadrupole time-of-flight mass spectrometry coupled to ultra-high-pressure liquid chromatograph was used for the screening and the structural elucidation of biodegradation products. A microbial metabolite of atenolol with [M+H](+) at 268 was detected in the positive electrospray ionization mode. This new compound was determined to be a product of microbial hydrolysis of the amide of the parent compound. Biodegradation of glibenclamide by activated sludge proceeded via bacterial hydroxylation of the cyclohexyl ring, which resulted in formation of metabolite with a protonated molecule, [M+H](+)=510. MS(3) experiments performed by hybrid quadrupole linear ion trap (QqLIT) mass spectrometry coupled to high-performance liquid chromatography enabled further structural elucidation of the identified metabolites. Moreover, the highly sensitive QqLIT instrument in the MRM mode enabled the detection of parent compounds and one of the microbial metabolites identified in real wastewater samples. The methodology used in this study permitted for the first time the identification and detection of biodegradation product of beta-blocker atenolol in real wastewater samples.