This paper presents the effects of protrusions on heat transfer in a microtube and in a two-dimensional microchannel of finite wall thickness. The effects of protrusion shape, size, and number were investigated. Calculations were done for incompressible flow of a Newtonian fluid with developing momentum and thermal boundary layers under uniform and discrete heating conditions. It was found that the local Nusselt number near a protrusion changes significantly with the variations of Reynolds number, height, width, and distance between protrusions, and the distribution of discrete heat sources. The results presented in the paper demonstrate that protrusions can be used advantageously for the enhancement of local heat transfer whereas the global performance may be enhanced or diminished based on the channel geometry.