Pressure drop and heat transfer characteristics of a periodically fully developed flow in the flat channel with protrusions are investigated. The effects of shape and location of protrusion on the pressure drop and heat transfer are numerically analyzed in the present study. Taguchi method is used to optimize these parameters. It is found that the ratio of the height of protrusion to channel height shows larger influence on the pressure drop and heat transfer than the ratio of the length of protrusion to module length. As the height of protrusion increases, pressure drop and heat transfer increase, but if the height of protrusion exceeds 2/3 of the channel height, there is a substantial pressure drop. The results also show that the optimal length and height of protrusion are half of the module length and half of the channel height, respectively.