The frog Xenopus is a well established vertebrate model to study the processes involved in embryogenesis and organogenesis, as it can be manipulated easily with a whole series of methods. We have expanded these approaches by establishing two transgenic Xenopus strains that allow specific interference with the activity of defined genes using a heat-shock inducible Cre recombinase that can induce upon heat-shock expression of a reporter gene in crossings to a corresponding reporter strain. We have applied this binary technique of gene interference in Xenopus development to overexpress the mutated HNF1β transcription factor at distinct developmental stages. Induction of HNF1β P328L329del by heat-shock at the gastrula stage resulted in a dramatic phenotype including malformation of the pronephros, gut, stomach, abnormal tail development and massive edemas indicative for kidney dysfunction. Thus, we have established the first binary inducible gene expression system in Xenopus laevis that can be used to study organogenesis.