The Drosophila eyes absent (eya) gene has a role in regulating cell death and/or differentiation and is expressed throughout development. We evaluated the transcripts and proteins encoded by one of the human homologues of Drosophila eya coined Eyes Absent 2 (EYA2). Interestingly, EYA2 was expressed in several neuroblastoma cell lines as four distinct transcripts having alternative 5'-ends, whereas only one EYA2 transcript was expressed in the normal human eye. Due to different translation start sites on the four unique transcripts, two isoforms of EYA2 protein (one previously identified and one novel) could be generated in neuroblastoma cells, but the sole EYA2 transcript expressed in the eye can only encode the novel isoform. Immunoblot analyses suggest that EYA2 may also be post-translationally modified. Finally, the alternative EYA2 transcripts have dissimilar numbers of upstream open reading frames in their 5'-untranslated regions. Therefore, in addition to encoding alternative isoforms of EYA2, regulation of EYA2 expression appears to involve both transcriptional and translational components.