Objective We compared an infrared temporal artery thermometer with our clinical standard axillary thermometer for temperature measurements in neonatal patients. Study Design We measured temporal artery (T-ta), axillary (T-ax, clinical standard), and rectal (T-r, gold standard) temperatures of 49 infants. The difference between T-r and T-ta was compared with that between Tr and Tax, and the data were analyzed based on bed type and postmenstrual age. Results The mean T-ta, T-ax, and T-r were 37.16 (SD 0.36) degrees C, 36.61 (SD 0.30) degrees C, and 36.82 (SD 0.30) degrees C, respectively. The measurements by these methods were all significantly different. The mean T-r-T-ax was 0.21 (SD 0.26) degrees C, and the mean T-r-T-ta was -0.34 (SD 0.37) degrees C, indicating that Tax was closer to Tr than was Tta (p < 0.0001). T-ta agreed more closely with Tr for infants in cribs than for those in incubators. Adjusting for bed type and body weight, with each week of postmenstrual age, the discrepancy between T-r-T-ta and T-r-T-ax decreased by 0.005 degrees C (p = 0.034). Conclusion Compared with the gold standard, T-r, Tta is not more accurate than T-ax. The temporal artery thermometer was less accurate for infants in incubators than for infants in cribs. The accuracy of temporal artery temperature increased with postmenstrual age.