Hedgehog and Wnt proteins are signaling molecules that direct many aspects of metazoan development through signal transduction pathways that are just beginning to be understood. Recently, the common use of glycogen synthase kinase 3 and casein kinase 1 has been added to a growing list of straightforward similarities between Hedgehog and Wnt signaling pathways. These kinases silence both pathways by labeling a key transcription factor (Cubitus interruptus) or co-activator (beta-catenin) for proteolysis, and it is possible that reversal of these phosphorylation events is, in each case, central to pathway activation. This review compares the two pathways to explore whether our more extensive knowledge of Wnt pathways can be of predictive value for investigating Hedgehog signaling.