In this study, the three-dimensional fluid flow and heat transfer in a rectangular micro-channel heat sink are analyzed numerically using water as the cooling fluid. The heat sink consists of a 1-cm(2) silicon wafer. The micro-channels have a width of 57 mum and a depth of 180 mum, and are separated by a 43 mum wall. A numerical code based on the finite difference method and the SIMPLE algorithm is developed to solve the governing equations. The code is carefully validated by comparing the predictions with analytical solutions and available experimental data. For the microchannel heat sink investigated, it is found that the temperature rise along the flow direction in the solid and fluid regions can be approximated as linear. The highest temperature is encountered at the heated base surface of the heat sink immediately above the channel outlet. The heat flux and Nusselt number have much higher values near the channel inlet and vary around the channel periphery, approaching zero in the corners, Flow Reynolds number affects the length of the flow developing region. For a relatively high Reynolds number of 1400, fully developed flow may not be achieved inside the heat sink. Increasing the thermal conductivity of the solid substrate reduces the temperature at the heated base surface of the heat sink,, especially near the channel outlet. Although the classical fin analysis method provides a simplified means to modeling heat transfer in micro-channel heat sinks, some key assumptions introduced in the fin method deviate significantly from the real situation, which may compromise the accuracy of this method.