Congenital heart defects (CHD) affect around 1% of live births, approximating in around 100 children born each year in Estonia with CHD. Advances in medical knowledge and technology have ameliorated diagnostics and risen life-expectancy of these patients well into adulthood. Each patient with CHD needs an individualised approach from diagnosis to custom-made treatment and follow-up plan to achieve the best results. This article highlights the peculiarities, challenges and possible suggestions in managing such patient population in a small country with rather low number of cases. Maximal concentration of expertise in one specialized center seems like most appropriate option to provide optimal care.