Pitx2 is expressed in developing visceral organs on the left side and is implicated in left-right (LR) asymmetric organogenesis. The asymmetric expression of Pitx2 is controlled by an intronic enhancer (ASE) that contains multiple Foxh1-binding sites and an Nkx2-binding site. These binding sites are essential and sufficient for asymmetric enhancer activity and are evolutionarily conserved among vertebrates. We now show that mice that lack the ASE of Pitx2 (Pitx2(Delta)(ASE/)(Delta)(ASE) mice) fail to manifest left-sided Pitx2 expression and exhibit laterality defects in most visceral organs, although the position of the stomach and heart looping remain unaffected. Asymmetric Pitx2 expression in some domains, such as the common cardinal vein, was found to be induced by Nodal signaling but to be independent of the ASE of Pitx2. Expression of Pitx2 appears to be repressed in a large portion of the heart ventricle and atrioventricular canal of wild-type mice by a negative feedback mechanism at a time when the gene is still expressed in its other domains. Rescue of the early phase of asymmetric Pitx2 expression in the left lateral plate of Pitx2(Delta)(ASE/)(Delta)(ASE) embryos was not sufficient to restore normal organogenesis, suggesting that continuous expression of Pitx2 in the lineage of the left lateral plate is required for situs-specific organogenesis.