Although mortality rates for patients with d-transposition of the great arteries remain quite low, these patients have a unique circulation that requires careful management in the peri-operative period. Despite the improved mortality for patients with common arterial trunk, the course in the intensive care unit is remarkable for significant morbidity and utilisation of significant resources. Pre-operative patient management focuses on balancing competing circulations, pulmonary and systemic, which exist in parallel rather than in series, as in the normal circulation. Post-operative patient management in both lesions focuses on optimising systemic output, respiratory status, and mitigating the effects of cardiopulmonary bypass. In this article, we review pre- and post-operative intensive care management in neonates with d-transposition of the great arteries and common arterial trunk.