Despite an externally symmetric body plan, the internal viscera of all vertebrates are asymmetric with respect to the left-right body axis. Determination of the handedness of this asymmetry is nonrandom and highly conserved among vertebrates. Errors in patterning along the left-right axis, which occur in about 1 in 10,000 human births, may result in significant morbidity and mortality. During early embryonic development, midline structures, in particular the node, coordinate patterning of the three main embryonic axes: anterior-posterior, dorsal-ventral, and left-right. A current model for specification of the handedness of left-right axis asymmetry invokes the activity of embryonic cilia in the node that create a net leftward flow of extraembryonic fluid. This flow is proposed to provide a signal for subsequent asymmetric gene expression. Signaling from the node defines patterns of asymmetric gene expression on the left and right sides of the embryo. These signals for “left” and “r ight” are ultimately interpreted by organ primordia during later development. Complex activating and inhibiting interactions involving TGF-β family members, as well as homeobox transcription factors, mediate these asymmetric patterns of gene expression. The identification of the genes regulating left-right axis patterning in model organisms has resulted in the characterization of human mutations associated with left-right axis malformations.