A highly sensitive liquid chromatography-tandem mass spectrometry method was developed and validated for the determination of limonin in human urine using podophyllotoxin as internal standard. The analyte and IS were extracted with solid-phase extraction and separated by a rapid isocratic elution with 1% formic acid/methanol (v:v, 40:60) on an C(18) column (150 mm × 2.1 mm I.D.). The detection was performed by mass spectrometry in the multi-reaction-monitoring mode. The precursor to product ion transitions of m/z 471.3→161.2 and m/z 397.2→313.1 were used to measure the analyte and the IS. The assay was linear over the concentration range of 0.0783-10 ng/mL for limonin in human urine. The lower limit of quantification was 0.0783 ng/mL and the extraction recovery was larger than 76.7% for limonin. The inter- and intra-day precision of the method at three concentrations was less than 7.4%. The method was successfully applied to pharmacokinetic study of limonin in humans.