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A sensitive and selective method using liquid chromatography-electrospray mass spectrometry (LC-ESI-MS) for the determination of carbadox metabolites, quinoxaline-2-carboxylic acid (QCA) and desoxycarbadox (Desoxy-CDX), in swine muscle and liver has been developed. The LC separation was performed on a Cadenza CD-C18 column (10 cm x 2 mm i.d.) with a gradient system of 0.01% acetic acid-acetonitrile as the mobile phase at a flow rate of 0.2 mL/min. Negative ionization produced the [M - H](-) molecular ion of QCA. On the other hand, the positive mode produced the [M + H](+) ion of Desoxy-CDX. The calibration graphs for QCA and Desoxy-CDX were rectilinear from 0.01 to 0.5 ng with selected ion monitoring (SIM). The drugs were extracted with 0.3% metaphosphoric acid-methanol (7: 3), and the extracts were cleaned up on an Oasis HLB cartridge (60 mg) and by liquid-liquid extraction. The recoveries of QCA and Desoxy-CDX from swine muscle and liver fortified at 2.5 and 5 ng/g were 70.2-86.3%, and the detection limits were 1 ng/g for both drugs.