The most obvious manifestation of the existence of a segmented, or metameric, body plan in vertebrate embryos is seen during the formation of the somites. Somites are transient embryonic structures formed in a progressive manner from a nonsegmented mesoderm in a highly regulated process called somitogenesis. As development proceeds different compartments are formed within each somite and these progressively follow a variety of differentiation programs to form segmented organs, such as the different bones that make the axial skeleton, body skeletal muscles and part of the dermis. Transcription factors from the basic helix-loop-helix (bHLH) protein family have been described to be implicated in each of the processes involved in somite formation. bHLH proteins are a family of transcription factors characterized by the presence of a DNA binding domain and a dimerization motif that consists of a basic region adjacent to an amphipathic helix, a loop and a second amphipathic helix. In this chapter we will review a number of bHLH proteins known to play a role in somitogenesis.