An isotope-dilution electrospray ionization tandem mass spectrometry (ESI-MS/MS) method with an on-line sample clean-up device, for the quantitative analysis of human urine for the benzene exposure biomarker S-phenylmercapturic acid (SPMA), was developed and validated. The sample clean-up system was constructed from an autosampler, a reversed-phase C18 trap cartridge, a two-position switching valve, and controlling computer software and hardware. The sample clean-up system was interfaced via 1/20 splitting to the ESI source of a triple-quadrupole mass spectrometer using negative ion mode and multiple reaction monitoring for SPMA and the isotope-labeled internal standard. A strategy was adopted to acquire pooled blank urine matrix and quality control samples spiked with standards. Validated procedures and data on method specificity, detection limits, standard curves, precision and recovery, sample storage stability, and inter-laboratory comparison are presented. The analytical system was fully automated. No tedious manual sample clean-up procedures are required. With the selectivity and the sensitivity provided by ESI-MS/MS detection, the analytical system can be used for high-throughput and accurate determination of SPMA levels in human urine samples, as a biomarker for environmental as well as occupational benzene exposure.