A new method recently used for measuring the temperature is using tympanic thermometer. The aim of this study was to compare the accuracy of this method with rectal and axillary measurement in children less than 6 years old. A total of 220 pair ears, axillaries, and rectal sites were used to determine the body temperature in patients aged between 3 months to 6 years who referred to Emergency Department of Fateme Zahra Hospital affiliated to Bushehr University of Medical Sciences. Rectal temperature (RT) was considered as gold standard. Fever was defined as RT >= 38 degrees C, axillary temperature (AT) 3 37.2 degrees C and tympanic temperature (TT) >= 38 degrees C. Correlation between rectal and tympanic temperature was statistically significant. The mean difference between RT and TT was 0.3 degrees C and between RT and AT was 0.1 degrees C. When cutoff point was considered 38 degrees C for TT, the sensitivity was 46%, specificity was 97% and positive predictive value (PPV) and negative predictive value (NPV) were 92% and 72% respectively. ROC curve showed the best cutoff point for TT as 37 degrees C, which increased the sensitivity to 92% and PPV to 0.98 but decreased the specificity to 90% and NPV to 0.57. Kappa test showed a good agreement rate between RT and TT. Age had significant effects on the TT/RT relationship. If the cut off point for TT is set at 38 degrees C the sensitivity and NPV will be unacceptably low and a number of children with fever may be missed by screening with a tympanic thermometer. If the cutoff point is 37 degrees C, the sensitivity and NPV will improve and TT can be used as a safe, easy, rapid, and accurate method in pediatrics.