Because of health concerns surrounding widespread exposure to perchlorate, we developed a sensitive and selective method for quantifying perchlorate in human urine using ion chromatography coupled with electrospray ionization tandem mass spectrometry. Perchlorate was quantified using a stable isotope-labeled internal standard ((18)O(4)-perchlorate) with excellent assay precision (coefficient of variation <5% for repetitively analyzed quality control material). Analytical accuracy was established by blind analysis of certified proficiency testing materials prepared in synthetic urine matrix; calculated amounts deviated minimally from true amounts, with percent differences ranging from 2% to 5%. Selective chromatography and tandem mass spectrometry reduced the need for sample cleanup, resulting in a rugged and rapid method capable of routinely analyzing 75 samples/day. The lowest reportable level (0.025 ng/mL) was sufficiently sensitive to detect perchlorate in all human urine samples evaluated to date, with a linear response range from 0.025 to 100 ng/mL. This selective, sensitive, and rapid method will help elucidate any potential associations between human exposure to low levels of perchlorate and adverse health effects.