13-Tubulin mRNAs associated with cilium formation in Strongylocentrotus purpurpatus sea urchin embryos are expressed selectively from a multiple gene family. The accumulations of three 13-tubulin mRNAs (131, 132, and 133) are temporally coordinated with ciliogenesis during blastula development and with the regeneration of cilia after their amputation. In contrast, another 13-tubulin mRNA, 134, is not induced in either case. The zincanimalized embryo with its exaggerated blastula phenotype forms longer cilia through a protracted period of ciliogenesis, in which the 13-tubulin mRNAs, principally 131, accumulate to higher than normal levels. The rate of 13-tubulin transcription per nucleus in the animalized embryo is greater than that of the normal embryo and is not changed through deciliation, although the tubulin mRNAs accumulate to higher levels. However, deciliation raises the 13-tubulin transcription rate in the normal embryo to that in the animalized embryo. Thus, the induction of 13-tubulin mRNA by cilium amputation is regulated transcriptionally in the normal embryo, but post-transcriptionally in the zinc-animalized embryos. Moreover, the 13-tubulin genes that are expressed in association with cilium formation appear to be induced selectively within the framework of ectodermal celltype specificity.