Heart morphogenesis involves sequential anatomical changes from a linear tube of a single channel peristaltic pump to a four‐chamber structure with two channels controlled by one‐way valves. The developing heart undergoes continuous remodeling, including septation. Pitx2‐null mice are characterized by cardiac septational defects of the atria, ventricles, and outflow tract. Pitx2‐null mice also exhibited a short outflow tract, including unseptated conus and deformed endocardial cushions. Cushions were characterized with a jelly‐like structure, rather than the distinct membrane‐looking leaflets, indicating that endothelial mesenchymal transition was impaired in Pitx2^−/− embryos. Mesoderm cells from the branchial arches and neural crest cells from the otic region contribute to the development of the endocardial cushions, and both were reduced in number. Members of the Fgf and Bmp families exhibited altered expression levels in the mutants. We suggest that Pitx2 is involved in the cardiac outflow tract septation by promoting and/or maintaining the number and the remodeling process of the mesoderm progenitor cells. Pitx2 influences the expression of transcription factors and signaling molecules involved in the differentiation of the cushion mesenchyme during heart development. Developmental Dynamics 242:456–468, 2013. © 2013 Wiley Periodicals, Inc.