We present a numerical study of the effects of surface roughness, which is unavoidable due to manufacturing tolerance, on laminar flow and heat transfer in microchannels. Three different channel types namely, square channel, wavy channel and dimpled channel are studied. Surface roughness is modeled as a superposition of waves described by Fourier series and exponential correlation function. Up to 2% relative roughness is introduced to one of the four side walls. We introduce the surface roughness by meshing a smooth channel. The boundary nodes are then displaced to introduce surface roughness. Periodic boundaries are used to study the flow and heat transfer features in the fully developed region. The Reynolds number keeps at 500, and 0.5 W/mm2 heat flux is adopted on the bottom of heat sinks. Results show that roughness could increase the overall flow resistance and Nusselt number. While relative roughness is about 2%, pressure drop increased by 3%, 5.3%, 5.9%, Nusselt number increased by 10%, 6.5%, 19.8% in square channel, wavy channel and dimpled channel respectively. Moreover, local influence of roughness highly depends on the geometric shape of the microchannel. The simulation results are expected to provide guidance to roughness control in microchannel manufacturing.