In this study, the effect of thermal radiation on micro-polar fluid flow over a wavy surface is studied. The optically thick limit approximation for the radiation flux is assumed. Prandtl’s transposition theorem is used to stretch the ordinary coordinate system in certain directions. The wavy surface can be transferred into a calculable plane coordinate system. The governing equations of micro-polar fluid along a wavy surface are derived from the complete Navier-Stokes equations. A simple transformation is proposed to transform the governing equations into boundary layer equations so they can be solved numerically by the cubic spline collocation method. A modified form for the entropy generation equation is derived. Effects of thermal radiation on the temperature and the vortex viscosity parameter and the effects of the wavy surface on the velocity are all included in the modified entropy generation equation.