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Perchlorate (ClO4−) is a ubiquitous environmental contaminant with high human exposure potential; it has both natural and man-made sources in the environment. Natural perchlorate forms in the atmosphere from where it deposits onto the surface of Earth, whereas synthetic perchlorate is manufactured as an oxidant for industrial, aerospace, and military applications. Perchlorate exposure can potentially cause adverse health effects in humans by interfering with the production of thyroid hormones through competitively blocking iodide uptake. To control and reduce perchlorate exposure, the contributions of different sources of perchlorate exposure need to be quantified. Thus, we demonstrate a novel approach for determining the contribution of different perchlorate exposure sources by quantifying stable and radioactive chlorine isotopes of perchlorate extracted from composite urine samples from two distinct populations: one in Atlanta, USA and one in Taltal, Chile (Atacama region). Urinary perchlorate from the Atlanta region resembles indigenous natural perchlorate from the southwestern USA [δ37Cl = +4.1 ± 1.0 ‰; 36Cl/Cl = 1811 (± 136) × 10−15], and urinary perchlorate from the Taltal, Chile region is similar to natural perchlorate in nitrate salt deposits from the Atacama Desert of northern Chile [δ37Cl = −11.0 ± 1.0 ‰; 36Cl/Cl = 254 (± 40) × 10−15]. Neither urinary perchlorate resembled the isotopic pattern found in synthetic perchlorate. These results indicate that natural perchlorate of regional provenance is the dominant exposure source for the two sample populations, and that chlorine isotope ratios provide a robust tool for elucidating perchlorate exposure pathways.