Recent gene targeting studies have revealed unexpected roles for endothelins in the development of neural crestderived tissues. Endothelin converting enzyme-1 (ECE-1) catalyzes the proteolytic activation of big endothelin-1 to endothelin-1(ET-1) in vitro. However, the importance of ECE-1 cleavage in the multiple endothelin pathways in vivo is unknown. Here we generated a targeted null mutation in the mouse ECE-1 gene. ECE-1^−/− term embryos exhibited craniofacial and cardiac abnormalities virtually identical to the defects seen in ET-1 and endothelin A receptor (ET_A)deficient embryos. Epidermal melanocytes as well as enteric neurons of the distal gut were also absent in ECE-1^−/− embryos, reproducing the developmental phenotype seen in ET-3^−/− and endothelin B receptor (ET_B)^−/− mice. Surprisingly, large amounts of mature ET-1 peptide are found in ECE-1^−/− embryos, indicating that non-ECE-1 protease(s) can activate ET-1 at certain sites. However, these enzymes cannot produce sufficient mature endothelin at the locations crucial for normal embryonic development. These findings reveal that ECE-1 is a bona fide activating protease for both big ET-1 and big ET-3 in vivo, and that the cell-cell communication pathways represented by the ET-1/ECE-1/ET_A axis and the ET-3/ECE-1/ET_B axis are each involved in the development of distinct subsets of neural crest cell lineages. Mutations in ECE-1 may cause developmental defects in humans, such as Hirschsprung disease, velocardiofacial syndrome and related neurocristopathies.