Background: Babies with cardiovascular malformations are usually asymptomatic at birth. Earlier diagnosis is likely to lead to a better outcome. This study examines trends in the timing of diagnosis of potentially life-threatening cardiovascular malformations. Methods: Ascertainment of all cardiovascular malformations diagnosed in infancy in the resident population of one English health region in 1985–2004. Babies considered to have a life-threatening cardiovascular malformation included all those with hypoplastic left heart, pulmonary atresia with intact ventricular septum, transposition of the great arteries, or interruption of the aorta; and babies dying or undergoing operation in the first 28 days with coarctation of the aorta, aortic stenosis, pulmonary stenosis, tetralogy of Fallot, pulmonary atresia with ventricular septal defect, or total anomalous pulmonary venous connection. Results: Of 688,167 live born babies in the 20 years of the study, 4444 had cardiovascular malformations diagnosed in infancy (6.5 per 1000). Cardiovascular malformations were potentially life-threatening in 685 (15%). Over the time of the study, 8% were recognised prenatally, 58% postnatally before discharge from hospital, 31% in life after discharge and 3% after death. Malformations most likely to remain undiagnosed at discharge were coarctation of the aorta (63%), interruption of the aortic arch (50%), and total anomalous pulmonary venous connection (47%). Over the 20 years of the study, the proportion of babies diagnosed antenatally increased from around 1% to 20% and no case was first diagnosed after death in the last 10 years. However, the recent proportion going home without a diagnosis remains around 25%. Conclusions: Overall one third of babies with potentially life-threatening cardiovascular malformations leave hospital undiagnosed. In recent years better antenatal diagnosis has reduced this proportion to one quarter. Better early recognition of such babies is unlikely to be achieved by clinical examination and is more likely to come from further improvements in antenatal diagnosis and more widespread adoption of routine pulse oximetry.