Perchlorate, an inorganic anion, has recently been recognized as an environmental contaminant by the US Environmental Protection Agency. Urine is the preferred matrix for assessment of human exposure to perchlorate. Although the measurement technique for perchlorate in urine was developed in 2005, the calibration and quality assurance aspects of the metrology infrastructure for perchlorate are still lacking in that there is no certified reference material (CRM) traceable to the International System of Units. To meet the quality assurance needs in biomonitoring measurements of perchlorate and the related anions that affect thyroid health, the National Institute of Standards and Technology (NIST), in collaboration with the Centers for Disease Control and Prevention (CDC), developed Standard Reference Material (SRM) 3668 Mercury, Perchlorate, and Iodide in Frozen Human Urine. SRM 3668 consists of perchlorate, nitrate, thiocyanate, iodine, and mercury in urine at two levels that represent the 50th and 95th percentiles, respectively, of the concentrations (with some adjustments) in the US population. It is the first CRM being certified for perchlorate. Measurements leading to the certification of perchlorate were made collaboratively at NIST and CDC using three methods based on liquid or ion chromatography tandem mass spectrometry. Potential sources of bias were analyzed, and results were compared for the three methods. Perchlorate in SRM 3668 Level I urine was certified to be 2.70 ± 0.21 μg L(-1), and for SRM 3668 Level II urine, the certified value is 13.47 ± 0.96 μg L(-1).