Experiments were conducted to investigate heat transfer characteristics of water flowing through trapezoidal silicon microchannels with a hydraulic diameter ranging from 62 to 169 mu m. A numerical analysis was also carried out by solving a conjugate heat transfer problem involving simultaneous determination of the temperature field in both the solid and the fluid regions. The experimental results were compared with the numerical predictions and a significant difference was found. The comparison results indicated that the experimentally determined Nusselt number is much lower than that given by the numerical analysis. The measured lower Nusselt numbers may be due to the effects of surface roughness of the microchannel walls. Based on a roughness-viscosity model established in our previous work, a modified relation which accounts for the roughness-viscosity effects was proposed to interpret the experimental results.