An accelerating accumulation of recent data suggests that enhancers, the principal architects of transcriptional regulation, are as important as protein-coding sequences in the etiology of developmental diseases. Conditional knockout of murine Shox2 in limbs specifically disrupts chondrogenesis and the development of the humerus and femur, and is phenotypically similar to human SHOX-deficient patients, albeit different proximodistal locations are affected. Although we now have some understanding of the mechanism of Shox2 function in limb patterning, the molecular underpinnings of the cis-regulation of Shox2 to instruct stylopod development are unknown. We wished to identify enhancers that regulate Shox2 expression in limbs and subsequently delineate the limb-specific cis-regulatory topology of Shox2 utilizing a combination of different criteria for enhancer identification. In addition to enhancer-associated epigenetic signature profiling, we have utilized circular chromosome conformation capture (4C-seq) technology to probe the entire cis-regulatory organization of the Shox2 gene during limb development. We show five of numerous genomic regions within a 1.5 megabase (Mb) chromosomal territory surrounding the Shox2 gene that interact with this gene during limb development to drive similar Shox2-like limb lacZ activity in transgenic mice. The sequences we have identified will facilitate the search for transcription factors regulating Shox2 expression. Indeed, we found several previously determined GLI3 binding regions (Vokes et al., 2008) to overlap with a subset of characterized Shox2 limb enhancers and with the Shox2 gene, suggesting that hedgehog signalling may be a regulatory input for this gene’s expression. Genetic examination of composite Shox2/Gli3 and Shox2/Shh mutations show Shox2 to cooperate with Gli3 and Shh to pattern the stylopod.