Patients with congenital heart disease (CHD) associated with heterotaxy require high-risk surgical repairs. We recently showed such patients have increased post-surgical morbidity and respiratory complications. Heterotaxy is characterized by discordant abdominal/thoracic organ situs due to aberrant left-right patterning, a developmental process dependent on motile cilia in the embryonic node. As mucociliary clearance requires airway cilia motion, and we previously found a 40% incidence of CHD and heterotaxy in a mouse model of primary ciliary dyskinesia (PCD), we hypothesized PCD may have increased prevalence in heterotaxy patients. To test this hypothesis, we recruited 26 patients with CHD and heterotaxy, and evaluated for PCD with nasal nitric oxide (nNO) measurements and nasal biopsies for ciliary motion and electron microscopy (EM). Most CHD consisted of 9 poly/asplenia and in addition 7 non-HLHS single ventricles. Panel review of nNO, ciliary motion and EM data led to a consensus diagnosis of probable or possible ciliary dysfunction in 50% of patients. 6 with low nNO and ciliary dysmotility were designated probable PCD and 7 with borderline low nNO and/or aberrant ciliary motion distinct from classic PCD were designated possible PCD. Given heterotaxy and PCD are rare diseases each with incidences of 1/15,000, these findings indicate some heterotaxy may be a ciliopathy. These findings suggest heterotaxy patients undergoing cardiac surgery should have a PCD work-up. Those with confirmed ciliary dysfunction may be offered pulmonary therapies to improve mucociliary clearance. Such change in the standard of care may improve outcomes for heterotaxy patients undergoing high-risk cardiac surgery.