MOTIVATION: Probabilistic motif detection requires a multi-step approach going from the actual de novo regulatory motif finding up to a tedious assessment of the predicted motifs. MotifSuite, a user friendly web interface streamlines this analysis flow. Its core consists of two post processing procedures that allow prioritizing the motif detection output. The tools offered by MotifSuite are built around the well established motif detection tool MotifSampler, but can also be used in combination with any other probabilistic motif detection tool. Elaborate guidelines on each of its applications have been provided. AVAILABILITY: http://homes.esat.kuleuven.be/~bioi_marchal/MotifSuite/Index.htm CONTACT: email@example.com.