Liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for analysis of drugs and their metabolites. We used a column-switching system in combination with atmospheric pressure chemical ionization LC-MS (LC-APCI-MS) for the determination of theophylline and its metabolites in biological samples. The separation was carried out on a reversed-phase column using methanol-20 mM ammonium acetate as a mobile phase at a flow-rate of 1 ml/min in 30 min. In the mass spectrum, the molecular ions of these drugs and metabolites were clearly observed as base peaks. This method is sufficiently sensitive and accurate for the pharmacokinetic studies of these drugs.