eyes absent/Eya is a conserved transcriptional coactivator involved in development of various tissues and organs in arthropods and vertebrates. In Drosophila eye development, eya functions as part of the transcriptional regulatory network along with eyeless/Pax6, sine oculis/Six and dachshund/Dach. Here, we present the first functional study of the C. elegans Eya homolog, EYA-1. Loss of EYA-1 function by RNAi and deletion mutations resulted in early larval lethality with incomplete penetrance, associated with defects of differentiation and morphogenesis of several tissues and organs. In late embryogenesis, morphological defect in the head region, pharyngeal malformation and excess cell deaths in the anterior region were observed. Consistently, EYA-1 was expressed in the nuclei of a subset of anterior cells including pharyngeal and body wall muscle cells, starting from the morphogenesis stage in embryogenesis. Interestingly, eya-1 and pax-6/Pax6 mutants showed a strong genetic interaction for larval viability and embryonic anterior morphogenesis. Thus, eya-1 appears to play a partially redundant role with pax-6 during C. elegans embryogenesis.