Heat transfer coefficient in the entrance region of water flowing through micro-tubes with diameters of 962 μm and 123 μm was investigated in this study. Two temperature measurement methods, thermocouple and liquid crystal thermography (LCT), were used to measure the tube surface temperature. The experimental data showed mat the Nu in the entrance region can be predicted well by conventional correlation while using the LCT to measure the temperature. Using the temperature measurements from the thermocouples attached to the surface, the Nu is found to be significantly higher than the prediction. This was believed to be due to the error in measurement of temperature. Simulation results also revealed that the measured temperature for a small diameter tube can be significantly decreased with a thermocouple attached to it. In transition flow, the wall temperature was also found to have a significantly fluctuation, as large as 2 °C, due to the unsteady flow conditions, while for fully established laminar as well as turbulent flow conditions, the fluctuation was measured to be less than 0.2 °C The effect of viscous heating was negligible in the range of parameters investigated in this study.