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Accurate temperature readings, often obtained rectally, are an important part of the initial evaluation of pediatric patients in the Emergency Department. Temporal artery thermometry (TAT) is one way to noninvasively measure temperature. We sought to compare the accuracy of axillary and temporal artery temperatures compared to rectal.This prospective study included children age 0–36 months presenting to the Emergency Department of a large military treatment facility. Rectal, axillary, and temporal artery temperatures were obtained. Test characteristics (sensitivity, specificity, NPV, PPV) were reported. The effect of cutoff values 99.9 °F, 100.4 °F, and 102.2 °F on test characteristics were also evaluated.The sensitivities of axillary and temporal artery thermometry to detect rectal fever is 11.5% and 61.5% respectively. Cutoff values did not significantly alter test characteristics. In this study, temporal artery thermometry was 0.2 °C lower than rectal temperature, axillary measurement was 0.9 °C below the reference standard. Mean temperature difference in the febrile group between TAT and rectal thermometry was >0.5 °C compared with a mean temperature difference 0.05 °C in afebrile patients.The findings of our study do not support using axillary thermometry to screen pediatric patients for fever in the emergency department. TAT cannot be recommended as a rectal thermometry replacement where height and duration of fever are used in pediatric disease prediction models. TAT may have a role in screening for fever in the appropriate pediatric patient population like primary orthopedic or trauma presentations where the balance between device precision, data capture and patient comfort may favor use of TAT.