We report that targeted inactivation of the Eph receptor ligand ephrinB1 in mouse caused perinatal lethality, edema, defective body wall closure, and skeletal abnormalities. In the thorax, sternocostal connections were arranged asymmetrically and sternebrae were fused, defects that were phenocopied in EphB2/EphB3 receptor mutants. In the wrist, loss of ephrinB1 led to abnormal cartilage segmentation and the formation of additional skeletal elements. We conclude that ephrinB1 and B class Eph receptors provide positional cues required for the normal morphogenesis of skeletal elements. Another malformation, preaxial polydactyly, was exclusively seen in heterozygous females in which expression of the X-linked ephrinB1 gene was mosaic, so that ectopic EphB-ephrinB1 interactions led to restricted cell movements and the bifurcation of digital rays. Our findings suggest that differential cell adhesion and sorting might be relevant for an unusual class of X-linked human genetic disorders, in which heterozygous females show more severe phenotypes than hemizygous males.