The left-right body axis is coordinately aligned with the orthogonal dorsoventral and anterioposterior body axes. The developmental mechanisms that regulate axis coordination are unknown. Here it is shown that the cardiac left-right orientation in zebrafish (Danio rerio) is randomized in notochord-defective no tail and floating head mutants. no tail (Brachyury) and floating head (Xnot) encode putative transcription factors that are expressed in the organizer and notochord, structures which regulate dorsoventral and anterioposterior development in vertebrate embryos. Results from dorsal tissue extirpation and cardiac primordia explantation indicate that cardiac left-right orientation is dependent on dorsoanterior structures including the notochord and is specified during neural fold stages in Xenopus laevis. Thus, the notochord coordinates the development of all three body axes in the vertebrate body plan.