Primary cilia are required for signaling, chemosensing and mechanosensing in many fluid-filled organs, thus cilia could also have a direct role in heart development. They are essential to the development of cardiac left-right (LR) asymmetry by means of their function at the embryonic organizer (node). We show that cilia are found in the mouse embryo heart at embryonic day (e) 9.5-e12.5. We demonstrate abnormal development of the endocardial cushions (ECCs) and compact myocardium (CM) in e9.5 mouse embryos with absent cilia. In contrast, hearts from embryos with abnormal LR development due to paralyzed, but structurally normal, node cilia show less severe ECC defects and normal CM. These observations suggest that a subset of cilia called cardiac cilia are required in cardiac development independently from their function in LR development. One possible function of cardiac cilia is as mechanosensors, integrating flow, cardiac function, and morphogenesis.