We employed the yeast two-hybrid technique to screen a mouse embryo cDNA library for novel tissue-specific Class B basic helix-loop-helix (bHLH) transcription factors, which heterodimerize with the ubiquitously expressed Class A bHLH protein E12. From this screen, we cloned a novel bHLH protein, which we named eHAND. Its low sequence identity with other bHLH family members and unique expression pattern during development suggest that eHAND defines a new subclass of Class B bHLH proteins. eHAND was expressed at high levels in trophoblast cells and extraembryonic membranes throughout development. The first site of eHAND expression in embryos was the heart, where it was expressed at high levels between 8.5 and 10.5 days post coitum (d.p.c.), after which transcript levels declined abruptly. By 13.5 d.p.c., eHAND expression in the heart was localized to regions of valve formation. Expression in other regions of the embryo was confined to tissues with a substantial neural crest component. eHAND was expressed in the first branchial arch and its derivatives, in the sympathoadrenal lineage, and in the enteric systems. The expression pattern of eHAND during development is distinct from that of other bHLH genes and suggests that it has a role in formation of extraembryonic tissues, heart, and neural crest derivatives.