Sea stars share many characteristics with vertebrates, including deuterostome type development. We previously reported that sea star larvae are capable of complete regeneration (with organogenesis) of missing body parts. Here we report the first application of whole-body cDNA subtractive hybridization for the identification of regeneration-specific gene expression in a deuterostome. We identified nine novel cDNAs from genes differentially expressed during early larval sea star regeneration, including a serine protease which may have a function similar to that of trypsin/plasmin-like proteases during vertebrate wound repair and regeneration. This study demonstrates that sea star larvae can provide a valuable new deuterostome model for the study of regeneration genetics, with potential applications in vertebrate regeneration.