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In the past few decades, an emerging role for cilia in the pathogenesis of CHD has been identified, but this topic still largely remains an unexplored area. Mouse forward genetic screens and whole exome sequencing analysis of CHD patients have identified enrichment for<jats:italic>de novo<\/jats:italic>mutations in ciliary genes or non\u2010ciliary genes, which regulate cilia\u2010related pathways, linking cilia function to aberrant cardiac development. Key events in cardiac morphogenesis, including left\u2013right asymmetric development of the heart, are dependent upon cilia function. Cilia dysfunction during left\u2013right axis formation contributes to CHD as evidenced by the substantial proportion of heterotaxy patients displaying complex CHD. Cilia\u2010transduced signaling also regulates later events during heart development such as cardiac valve formation, outflow tract septation, ventricle development, and atrioventricular septa formation. 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