MyoD is a member of the basic-helix-loop-helix (bHLH) transcription factor family, which regulates muscle determination and differentiation in vertebrates. While it is now well established that the MyoD gene is regulated by Sonic hedgehog, Wnts, and other signals, it is not known how MyoD transcription is initiated and maintained in response to these signals. We have investigated the cis control of MyoD expression to identify and characterize the DNA targets that mediate MyoD transcription in embryos. By monitoring lacZ reporter gene expression in transgenic mice, we show that regulatory information contained in 24 kb of human MyoD 5′ flanking sequence is sufficient to accurately control MyoD expression in embryos. Previous studies have identified two muscle-specific regulatory regions upstream of MyoD, a 4-kb region centered at −20 kb (designated fragment 3) that contains a highly conserved 258-bp core enhancer sequence, and a more proximal enhancer at −5 kb, termed the distal regulatory region (DRR), that heretofore has been identified only in mice. Here, we identify DRR-related sequences in humans and show that DRR function is conserved in humans and mice. In addition, transcriptional activity of MyoD 5′ flanking sequences in somites and limb buds is largely a composite of the individual specificities of the two enhancers. Deletion of fragment 3 resulted in dramatic but temporary expression defects in the hypaxial myotome and limb buds, suggesting that this regulatory region is essential for proper temporal and spatial patterning of MyoD expression. These data indicate that regulatory sequences in fragment 3 are important targets of embryonic signaling required for the initiation of MyoD expression. © 2001 Wiley-Liss, Inc.