Perchlorate is a naturally occurring inorganic anion used as a component of solid rocket fuel, explosives, and pyrotechnics. Sufficiently high perchlorate intakes can modify thyroid function by competitively inhibiting iodide uptake in adults; however, little is known about perchlorate exposure and health effects in infants. Food intake models predict that infants have higher perchlorate exposure doses than adults. For this reason, we measured perchlorate and related anions (nitrate, thiocyanate, and iodide) in 206 urine samples from 92 infants ages 1-377 days and calculated perchlorate intake dose for this sample of infants. The median estimated exposure dose for this sample of infants was 0.160 μg/kg/day. Of the 205 individual dose estimates, 9% exceeded the reference dose of 0.7 μg/kg/day; 6% of infants providing multiple samples had multiple perchlorate dose estimates above the reference dose. Estimated exposure dose differed by feeding method: breast-fed infants had a higher perchlorate exposure dose (geometric mean 0.220 μg/kg/day) than infants consuming cow milk-based formula (geometric mean 0.103 μg/kg/day, p < 0.0001) or soy-based formula (geometric mean 0.027 μg/kg/day, p < 0.0001), consistent with dose estimates based on dietary intake data. The ability of perchlorate to block adequate iodide uptake by the thyroid may have been reduced by the iodine-sufficient status of the infants studied (median urinary iodide 125 μg/L). Further research is needed to see whether these perchlorate intake doses lead to any health effects.