Bilateral pulmonary agenesis (PA) is a rare embryological defect incompatible with life. Unilateral PA has a wide range of clinical presentations: its prognosis depends on the presence and severity of other associated anomalies. Fetal biliary atresia has been associated with a number of congenital anomalies, but the etiology is still not understood. An unusual case of a child with right PA, right diaphragmatic hernia, and delayed diagnosed biliary atresia leading to liver failure is presented herein. At the age of 4 months the patient was referred to the Transplant Department at Children Healthcare of Atlanta at Egleston with cholestasis and failure to thrive. With a rapidly progressive liver insufficiency, this child was evaluated for liver transplantation. In the absence of any respiratory symptom, the patient received a deceased donor size-matched left lateral segment liver transplant, which covered the diaphragmatic defect, with no further repair required. Twenty-seven months post-transplant, the patient has good graft function, a normal Z-score and is thriving. In spite of the increased physiological and surgical challenges (absence of right lung tissue, hemi-diaphragm, and ectopic position of the liver in the right chest), liver transplantation was performed with positive outcome in this high-risk child. Whether PA, may have developmentally contributed to expression of biliary atresia will need further investigation.