The basic helix-loop-helix proteins form a special group of transcription factors unique for the eukaryotic organisms. They are crucial for the embryonic development of many fundamental organ systems such as muscle, heart, central nervous system, hematopoiteic system, and many others. They are very flexible in terms of regulating transcription in that they can either promote or repress transcription, and do so in many different ways. Basic helix-loop-helix proteins can form homo- or heterodimers with other members of the group, and are subject to post-transcriptional modifications. In this review, an overview of basic helix-loop-helix protein classification, biochemical function, and examples of past and recent advances in our understanding of embryonic development are presented, with emphasis on the vertebrate muscle, heart, brain, and eye.