This study discusses entropy generation analysis for a peristaltic flow in a rotating medium with generalized complaint walls. The goal of the current analysis is to understand the fluid flow phenomena particular to micro devices. Nano materials with a size less than 100 nm have applications in micro heat exchangers to cool electronic circuits, blood analyzers, biological cell separations, etc. For this study, we considered the effects of radiation, viscous dissipation and heat flux on the flow of nanomaterial inside a cylindrical micro-channel. To investigate the slip effects on the flow, the second order slip condition for axial velocity, the first order slip condition for secondary velocity and the thermal slip conditions were used. The flow was governed by partial differential equations (PDE’s), which were turned into a system of coupled ordinary differential equations (ODE’s) that were highly non-linear and numerically solved using the NDSolve command in Mathematica. The impacts of different involved parameters on the flow field were investigated with the aid of graphical illustrations. Entropy generation and the Bejan number were given special attention, and it was found that they decreased as the Hartman number, rotation, and radiation parameters increased.