To investigate the molecular regulation of embryonic somite formation and development, we have cloned the full-length cDNA and characterized the embryonic expression profile of chicken Paraxis, a member of a novel family of basic helix-loop-helix (bHLH) proteins, which has been suggested to play a role in paraxial mesoderm development. Chicken Paraxis encodes a 1.35-kb mRNA and contains a 53-amino-acid residue bHLH domain, identical in sequence to that found in the mammalian Paraxis genes of mouse, hamster, and human. Northern analysis revealed significant Paraxis expression in the early embryo up to the 30- to 35-somite stage, declining from Incubation Day 4 on and becoming undetectable by Day 5. By whole-mount in situ hybridization, Paraxis expression is first seen distinctly in the emerging paraxial mesoderm of the primitive streak stage chick embryo. During gastrulation, Paraxis expression in the mesoderm defines bilaterally symmetric crescents located immediately rostral to Hensen's node and appears to pre-configure the emerging somitic mesoderm. During somite development, Paraxis expression is evident in the rostral segmental plate and the newly formed somites, although the level of expression clearly decreases in the more mature somites. By the 10-12th pair of somites, counting from the caudal end, Paraxis expression appears to be preferentially localized to the medial aspect of individual somites. Histological analysis showed that Paraxis expression is evenly distributed in the newly formed caudal epithelial somites, then localized to the medial portion of maturing somites, and preferentially localized in the dermomyotome of more rostral somites before diminishing to undetectable levels in the most cranial somites. The functional involvement of Paraxis in somite development was assessed by perturbing its expression in somitic stage chick embryos using a Paraxis-specific antisense oligonucleotide. Disruption of somite formation from the paraxial mesoderm was observed in 67% of the surviving topically treated embryos, whereas control embryos treated with sense or random sequence oligonucleotides did not show similar effects. In addition, direct injection of Paraxis-specific antisense oligonucleotide into the paraxial mesoderm produced discrete segmentation anomalies which correlated spatially with the site of injection. Whole-mount in situ hybridization revealed that the regions defective in somite formation displayed perturbed Paraxis expression and a reduction of Pax-1 expression, a marker for epithelial somites and sclerotome. Histological analysis indicated poor condensation and/or epithelization of the somitic mesoderm. Finally, embryos treated with valproic acid, a known teratogen which affects somite segmentation, showed perturbed Paraxis expression, suggesting that the mechanism of action of this teratogen involves a pathway(s) requiring Paraxis activity. These data provide evidence that Paraxis acts as an important regulator of paraxial mesoderm and somite development and functions in axial patterning of the chick embryo.