To identify a regulatory role for proteolysis during early Xenopus development, we developed a biochemical screen for proteins that are degraded in an embryonic stage-specific manner. We found that Xom, a homeobox transcriptional repressor of dorsal-specific genes, was degraded precipitously during early gastrulation. Xom degradation is regulated by phosphorylation at a GSK3-like consensus site and is most likely mediated by the SCF-beta-TRCP complex. Expression of nondegradable Xom represses transcription of dorsal genes much more effectively than wild-type Xom and results in a more strongly ventralized phenotype. We propose that regulated Xom proteolysis plays an essential role in the establishment of the dorsoventral axis, by converting a gradient in BMP abundance into a sharp dorsoventral pattern.