Entropy generation in channels with non-uniform cross-section that can be found in many fluid flow systems is an important concern from the thermodynamic design point of view. In this regard, the entropy generation in channels with periodic wavy sinusoidal walls has been considered in the present study. The flow is assumed to be 2-D steady laminar and the main parameters considered are the Reynolds number, height ratio H-min/H-max and module length ratio L/a. The fluid enters the channel with uniform axial velocity and temperature. The wall of the channel is assumed to be at uniform temperature which is different that of the fluid at the inlet of the channel. The distribution of the entropy generation as well as the total entropy generation has been studied numerically. It is found that the Reynolds number and the geometric parameters, height ratio and module length ratio have significant effect on both the local concentrations of entropy generation as well as the total entropy generation in the channel. Flow separation and re-circulation size, strength and location of flow are found to be major concern in determining the local entropy generation.