Administration of pivalate-containing antibiotics decreases serum carnitine and increases urinary pivaloylcarnitine, resulting in hypocarnitinemia. Carnitine and acylcarnitines are important biomarkers in the diagnosis of carnitine deficiency, but the relationship between acylcarnitines and drug-induced hypocarnitinemia remains unclear. Quantification of acylcarnitines enables discovery of new biomarkers for prediction and diagnosis of drug-induced hypocarnitinemia. Here we describe a liquid chromatography/tandem mass-spectrometric method for simultaneously quantifying carnitine, 15 acylcarnitines, and cefditoren (the pivoxilated product of an antibiotic prodrug) in human urine. The matrix effect is corrected in 87.8-103% using deuterium-labeled internal standards (2H9-carnitine, 2H3-hexanoylcarnitine, and 2H3-stearoylcarnitine). The surrogate matrix method had an error of <13% in comparison with a standard addition method. Dynamic ranges were 0.1-100μmol/l for acylcarnitines and 0.3-300μg/ml for cefditoren. Both accuracy and precision were <19.7% at the lower limit of quantification and <14.8% for other quality controls. In an example application of this method, urine samples from eight healthy volunteers (five adults and three children) were analyzed, and individual differences were clearly observed.