Heterotaxy is a congenital abnormality where the internal thoraco-abdominal organs demonstrate abnormal arrangement across the left-right (L-R) axis of the body. It can affect the development of the heart, liver, lungs, intestines, and spleen. The L-R embryonic axis is established early in embryogenesis when unidirectional signals emanate from a specialised structure at the embryonic midline, called the node, to initiate distinct molecular pathways on the left and right sides of the developing embryo. The gene most commonly mutated in human cases of Heterotaxy is the X-linked ZIC3, but the mechanism by which the ZIC3 transcription factor prevents Heterotaxy remains unknown. A genetic screen for mutations that affect murine embryogenesis identified a novel null allele of Zic3, called katun (Ka). The mutant embryos exhibit Heterotaxy and also incompletely penetrant, partial (posterior) axis duplications and anterior truncation. These latter two phenotypes are redolent of elevated canonical Wnt signalling and analysis of Ka embryos reveals ectopic expression of direct targets of Wnt/β-catenin mediated transcription in mutant embryos. ZIC3 is a member of the Zic family of transcriptional regulators and previous work has shown that ZIC proteins can inhibit Wnt/β-catenin mediated transcription when overexpressed in cell lines. This raises the possibility that dysregulated Wnt signalling may contribute to Heterotaxy. We have investigated this notion by analysis of the murine batface (Bfc) gain-of-function allele of β-catenin that results in elevated Wnt/β-catenin signalling. We find this strain exhibits incompletely penetrant defects of L-R axis formation and synergises with the Zic3 Ka allele to produce an increased incidence of L-R axis defects. In both the Ka and Bfc strains, the node of homozygous embryos is misshapen and contains patches of non-ciliated cells that express endoderm genes. Moreover we find that human ZIC3-Heterotaxy associated mutations encode proteins that are defective in their ability to inhibit Wnt/β-catenin mediated transcription. Overall this provides strong evidence that Wnt dysregulation may underlie cases of ZIC3-associated Heterotaxy.