Gastrointestinal motility is ensured by the correct coordination of the enteric nervous system and the visceral smooth muscle cells (SMCs), and defective development of SMCs results in gut malformations and intestinal obstructions. In order to identify the molecular mechanisms that control the differentiation of the visceral mesenchyme into SMCs in the vertebrate stomach, we developed microarrays to analyze the gene expression profiles of undifferentiated and differentiated avian stomachs. We identify Scleraxis , a basic-helix-loop-helix transcription factor, as a new marker of stomach mesenchyme and find that expression of Scleraxis defines the presence of two tendons closely associated to the two visceral smooth muscles. Using targeted gene misexpression, we show that FGF signaling is sufficient to induce Scleraxis expression and to establish two tendon domains adjacent to the smooth muscle structures. We also demonstrate that the tendon organization is perturbed by altering Scleraxis expression or function. Moreover, using primary cells derived from stomach mesenchyme, we find that undifferentiated stomach mesenchyme can give rise to both SMCs and tendon cells. These data show that upon FGF activation, selected stomach mesenchymal cells are primed to express Scleraxis and to differentiate into tendon cells. Our findings identify a new anatomical and functional domain in the vertebrate stomach that we characterize as being two intermuscular tendons closely associated with the visceral SMC structures. We also demonstrate that the coordinated development of both tendon and smooth muscle domains is essential for the correct morphogenesis of the stomach.