Kidney organogenesis is initiated with the formation of the pronephric kidney and requires Pax-2 gene function. We report here the cloning and characterization of Pax-2 cDNAs from the frog Xenopus laevis, a model system suitable for the study of early kidney organogenesis. We show that expression of Xenopus Pax-2 (XPax-2) genes was confined to the nervous system, sensory organs, the visceral arches, and the developing excretory system. DNA sequencing of XPax-2 cDNAs isolated from head and pronephric kidney libraries revealed seven novel alternatively spliced Pax-2 isoforms. They all retain DNA-binding domains, but can differ significantly in their C termini with some isoforms containing a novel Pax-2 exon. We investigated the spectrum of XPax-2 splice events in pronephric kidneys, animal cap cultures and in whole embryos. Splicing of XPax-2 transcripts was found to be extensive and temporally regulated during Xenopus embryogenesis. Since all investigated tissues expressed essentially the full spectrum of XPax-2 splice variants, we conclude that splicing of XPax-2 transcripts does not occur in a tissue-specific manner.