The myogenic regulatory factors (MRFs), MyoD and myogenin, can induce myogenesis in a variety of cell lines but not efficiently in monolayer cultures of P19 embryonal carcinoma stem cells. Aggregation of cells expressing MRFs, termed P19[MRF] cells, results in an approximately 30-fold enhancement of myogenesis. Here we examine molecular events occurring during P19 cell aggregation to identify potential mechanisms regulating MRF activity. Although myogenin protein was continually present in the nuclei of >90% of P19[myogenin] cells, only a fraction of these cells differentiated. Consequently, it appears that post-translational regulation controls myogenin activity in a cell lineage-specific manner. A correlation was obtained between the expression of factors involved in somite patterning, including Wnt3a, Wnt5b, BMP-2/4, and Pax3, and the induction of myogenesis. Co-culturing P19[Wnt3a] cells with P19[MRF] cells in monolayer resulted in a 5- to 8-fold increase in myogenesis. Neither BMP-4 nor Pax3 was efficient in enhancing MRF activity in unaggregated P19 cultures. Furthermore, BMP-4 abrogated the enhanced myogenesis induced by Wnt signaling. Consequently, signaling events resulting from Wnt3a expression but not BMP-4 signaling or Pax3 expression, regulate MRF function. Therefore, the P19 cell culture system can be used to study the link between somite patterning events and myogenesis.