Eyes absent is essential for compound eye formation in Drosophila. Its mammalian homologues of Eya are involved in the development of sensory organs, skeletal muscles and kidneys. Mutations of EYA1 in human cause branchio-oto-renal syndrome, with abnormalities in branchial derivatives, ear and kidney. For an insight into the function of Eya1 and Eya2 in early development, we performed whole-mount in situ hybridization and compared the expression patterns of these two genes in the developing chick embryos. Eya1 was first expressed in the primitive streak at Hamburger and Hamilton stage 4 (HH4) and appeared in the ectoderm and head mesenchyme distinct from migrating neural crest cells at HH6-HH11. At HH15 and HH17, the olfactory, otic and vagal/nodose placodes and cranial ganglia were positive for Eya1. In contrast, Eya2 was already expressed in the endoderm at HH4, and appeared in the endoderm and prospective placodal region at HH6-HH11. Eya2 expression was observed in pharyngeal clefts and pouches as well as cranial placodes at HH15 and HH17. These results indicate differential expression of Eya1 and Eya2, both spatially and temporally, in chick during early development. The expression patterns are somewhat different from those of other species such as Xenopus, zebrafish and mouse. The results suggest distinct and unique functions for Eya1 and Eya2 in early chick development.