The avian eye is supported by a ring of evenly-spaced bony elements known as the scleral ossicles. The formation of these bones is directed by a series of conjunctival papillae, elongated epithelial structures that arise from placodes. Expression of some genes, such as β-catenin and the receptors for fibroblast growth factor (FGF), is known to occur in the developing conjunctival placodes and papillae (CPP). However, expression of genes from three other families important in epithelial placode systems, namely bone morphogenetic protein (BMP), ectodysplasin (EDA) and hedgehog (HH), was expected, although it had not been definitively shown. Therefore, the objective of this study was to analyze gene expression of the β-catenin, FGF, BMP, EDA and HH signalling pathways throughout CPP induction using a qPCR approach. The results indicate that at least two members of each of the five signalling pathways were expressed throughout CPP induction, with most genes exhibiting an initial increase in expression, followed by a decrease or a sustained expression level. Correlation analyses reveal the existence of two distinct gene interaction modules. Additionally, differences in gene expression among the temporal, nasal and dorsal regions were present for some genes. Therefore, a conserved signalling network is present in CPPs and other epithelial appendages and these signalling molecules have two patterns of expression, which may differ according to the specific eye region. The detailed spatiotemporal gene expression dynamics occurring throughout CPP induction are consistent with the presence of a molecular and potentially a mechanical patterning mechanism, as found in other placode systems.