The coupling of ultra high-pressure liquid chromatography with a single quadrupole mass spectrometer was investigated for the analysis of several cytochromes P450 (CYP450) substrates and respective metabolites. The effect of numerous operating parameters (e.g. mobile phase pH, flow rate, gradient length, MS acquisition mode, dwell time, polarity switching, etc.) on selectivity, sensitivity and acquisition rate was studied. It was demonstrated that basic pH conditions provided the best compromise in terms of sensitivity and chromatographic selectivity with both acidic and basic compounds. The optimal mobile phase flow rate for UHPLC-MS experiments should be comprised between 300 and 600 microL/min for 2.1mm ID columns, while a higher flow rate generated up to 3-fold loss in sensitivity. It was also demonstrated that the fast polarity switching mode represented a valuable tool to improve throughput, maintaining acceptable performance. Finally, limits of detection were included in the range [1-50 ng/mL] in positive ionization mode and [50-250 ng/mL] in negative ionization mode, for investigated compounds.