The molecular regulatory mechanisms underlying primary axis formation during sea urchin development have recently been identified. Two opposing maternally inherited systems, one animalizing and one vegetalizing, set up the animal-vegetal (A-V) axis. The vegetal system relies in part on the Wnt-beta-catenin-Tcf/Lef signaling pathway and the animal system is based on a cohort of animalizing transcription factors that includes members of the Ets and Sox classes. The two systems autonomously define three zones of cell-type specification along the A-V axis. The vegetalmost zone gives rise to the skeletogenic mesenchyme lineage; the animalmost zone gives rise to ectoderm; and the zone in which the two systems overlap generates endoderm, secondary mesenchyme, and ectoderm. Patterning along the A-V also depends on cellular interactions involving Wnt, Notch, and BMP signaling. We discuss how these systems impact the formation of the second axis, the oral-aboral axis; how they connect to later developmental events; and how they lead to cell-type-specific gene expression via cis-regulatory networks associated with transcriptional control regions. We also discuss how these systems may confer on the embryo its spectacular regulatory capacity to replace missing parts.