A common brachiocephalic trunk is an anatomic variant in which both common carotid arteries and the right subclavian artery arise from the aortic arch via a single trunk. The impact of this condition on associated congenital cardiac malformations is presently unknown. Out of a total of 1480 cardiac catheterizations performed in children over a period of 10 years, we discovered 48 patients (3.2%) to have a common brachiocephalic trunk, of whom 98% had associated congenital cardiac malformations. A spectrum of associated lesions was identified, including left-to-right shunts in 19 patients, right-sided anomalies in 18 patients, left-sided obstructive lesions in 12 patients, and coronary arterial abnormalities in 10 patients, eight of whom had other cardiac defects. Genetic syndromes were present in one-fifth of the cases. When found with left-sided malformations, the common trunk was associated with persistent hypoplasia of the aortic arch, likely related to diminished flow through the arch during development. In each of four patients in whom the brachiocephalic trunk had been used during construction of a palliative shunt, we observed inadequate growth and deformation of the pulmonary arteries. Thus, angiographic identification of a common brachiocephalic trunk may be a marker for the presence of accompanying congenital cardiac defects and coronary arterial abnormalities. Understanding the pathophysiologic effects of the common trunk is important when planning the palliative or corrective procedures, and when assessing the potential benefit of the surgical repair over the long term.