Hedgehog signalling regulates morphogenesis of many developing organs. Sonic hedgehog (Shh) signalling has been shown to regulate the growth and morphogenesis of the palatal shelves prior to their elevation and fusion. Here, we show that Shh expression is limited to a thickened palatal oral epithelium prior to palatal shelf elevation. After palatal shelf elevation above the tongue, Shh is expressed only in small areas of thickened palatal oral epithelium that corresponded to developing rugae. The receptor Ptc1 and a regulator of Hh signalling Hhip1 are expressed in the mesenchyme adjacent to the palatal oral epithelium so that the highest level of transcripts localize to the palatal mesenchyme surrounding the Shh-expressing thickened epithelium. Smoothened and transcriptional effectors Gli1-3, and Hh regulator Gas1 are expressed widely in the palatal mesenchyme. No differences were found in the expression patterns of Hh pathway members along the anterior-posterior axis of the developing palate.