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In this paper, viscous dissipation and roughness effects on heat transfer and fluid flow are investigated in microchannels using perturbation method in slip flow regime. The flow is considered to be laminar, developing thermally and hydrodynamically, two-dimensional, incompressible and steady-state. The working fluid is air, flowing between two parallel plates. The equations obtained from developing Navier-Stokes and energy equations are solved numerically according to different orders of Knudsen number, with second-order velocity slip and temperature jump boundary conditions. The effects of thermal creep has been ignored. Tempreture and velocity fields are obtained and estimated for both constatnt heat flux and constant wall tempreture. The effects of roughness height, space between roughness elements, roughness elements length, Re number and Kn number on slip behavior of gas flow are investigated.The results indicate considerable effect of viscous dissipation and roughness on fluid flow and heat transfer in microchannel.