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A sensitive and robust method using isotope dilution gas chromatography–electron capture negative chemical ionization mass spectrometry (GC–ECNI-MS) was developed and validated for the analysis of quinoxaline-2-carboxylic acid (QCA) in porcine liver. [ 2 H 4 ]QCA was added to liver samples which were then deproteinated with 2% metaphosphoric acid in 20% methanol. Followed by sequential extraction with water-saturated ethyl acetate and phosphate buffer, the buffer extracts were subject to solid-phase extraction clean-up by mixed mode anion-exchange columns. QCA was derivatized with N -methyl- N - tert -butyldimethylsilyltrifluoroacetamide (MTBSTFA) prior to GC–ECNI-MS determination. For unambiguous identification, a second GC–ECNI-MS experiment was performed on suspected positive samples which were derivatized independently with another derivatization agent, trimethylsilyldiazomethane. Excellent recovery and precision were obtained and the limit of quantitation was 0.7 μg/kg (S/N>60). Method ruggedness by Taguchi orthogonal array technique is also presented.