We have investigated the effects of geometry on the mixing performance of peristaltic micromixers. For the parametric study, we designed and fabricated eleven different mixers, varying the distance between the mixing valves, the mixing valve width, and the mixing loop shape. From the experimental parametric study, we derived design guidelines for a peristaltic micromixer. The guidelines would greatly improve the layout of the high-throughput integrated nanofluidic systems and overall performance by maximizing the mixing performance of the unit mixer.