The U.S. Food and Drug Administration's (FDA) Total Diet Study (TDS) monitors the US food supply for pesticide residues, industrial chemicals, radionuclides, nutrients, and toxic elements. Perchlorate and iodine intakes based on concentrations in TDS samples collected between 2008 and 2012 were estimated in order to update an earlier TDS dietary assessment. Perchlorate is used as an oxidizing agent in rocket and missile fuel, is formed naturally in the atmosphere, and occurs naturally in some soils. Because of perchlorate's presence in soil, and in irrigation, processing, and source water, it is widely found in food. Iodine was included in the study because perchlorate at high doses interferes with iodide uptake in the thyroid. Iodine (the elemental form of iodide) is essential for growth and development, and metabolism. This study uses a novel statistical method based on a clustered zero-inflated lognormal distribution model to estimate mean and 95th percentile confidence interval concentrations for perchlorate and iodine in US foods. These estimates were used to estimate mean perchlorate and iodine exposures for the total US population and for 14 age/sex groups in the US population. Estimated mean perchlorate intake for the total US population was 0.13 μg/kg bw/day, with mean intakes for the 14 age/sex groups between 0.09 and 0.43 μg/kg bw/day. The estimated mean intakes of perchlorate for all age/sex groups were below EPA's reference dose (RfD) of 0.7 μg/kg bw/day. The estimated mean iodine intake for the total US population was 216.4 μg/person/day, with mean intakes ranging from 140.9 to 296.3 μg/person/day for the 14 age/sex groups, with all age/sex groups exceeding their respective estimated average requirements (EARs).