Direct Numerical Simulations have been performed for turbulent flow in circular pipes with smooth and corrugated walls. The numerical method, based on second-order finite discretization together with the immersed boundary technique, was validated and applied to various types of flows. The analysis is focused on the turbulence kinetic energy and its budget. Large differences have been found in the near-wall region at low Reynolds number. The change in the near-wall turbulent structures is responsible for increase of drag and turbulence kinetic energy. To investigatselinae the effects of wall corrugations, the velocity fields have been decomposed so as to isolate coherent and incoherent motions. For corrugated walls, we find that coherent motions are strongest for walls covered with square bars aligned with the flow direction. In particular, the coherent contribution is substantial when the bars are spaced apart by a distance larger than their height. Detailed analysis of the turbulence kinetic energy budget shows for this set-up a very different behavior than for the other types of corrugations.