Experimental and numerical analysis were performed to evaluate heat transfer characteristics of water through five sets of rectangular microchannels. Microchannels of hydraulic diameter of 222 μm, 267 μm, 323 μm, 330 μm and 343 μm respectively for Re number between 2.1 to 48 were analysed. Numerical analysis and experiments were conducted under a input heat of 10 W to 100 W, inlet fluid temperature 29°C and mass flow rates of 0.0167 kg/sec to 0.116 kg/sec. Nusselt number tends to be linear increasing as Reynolds number increases. Besides high temperature gradient exist in the region between inlet and exit of flow microchannel. For hydraulic diameter 222 μm, heat transfer coefficient seems to be higher as compare to other configurations of hydraulic diameters. Numerical results showed reasonably good agreement within 4-5% with experimental results.