Disruption of the long-rangecis-regulation of developmental gene expression is increasingly recognized as a cause of human disease. Here, we report a novel type of long-rangecis-regulatory mutation, in which ectopic expression of a gene is driven by an enhancer that is not its own. We have termed this gain of regulatory information as “enhancer adoption.” We mapped the breakpoints of a de novo 7q inversion in a child with features of a holoprosencephaly spectrum (HPES) disorder and severe upper limb syndactyly with lower limb synpolydactyly. The HPES plausibly results from the 7q36.3 breakpoint dislocating the sonic hedgehog (SHH) gene from enhancers that are known to drive expression in the early forebrain. However, the limb phenotype cannot be explained by loss of knownSHHenhancers. TheSHHtranscription unit is relocated to 7q22.1, ˜190 kb 3′ of a highly conserved noncoding element (HCNE2) within an intron ofEMID2. We show that HCNE2 functions as a limb bud enhancer in mouse embryos and drives ectopic expression ofShhin vivo recapitulating the limb phenotype in the child. This developmental genetic mechanism may explain a proportion of the novel or unexplained phenotypes associated with balanced chromosome rearrangements. 32:1492–1499, 2011. ©2011 Wiley Periodicals, Inc.