Cyclosporin A is the primary immunosuppressive agent used in cardiac transplantation to maintain chronic immunosuppression. Absorption may be erratic and major side-effects include nephrotoxicity. A recently introduced formulation (Neoral) improves absorption in cystic fibrosis heart-lung transplant recipients, but episodes of rejection have been reported on conversion from the oil-based formulation. A retrospective analysis of 21 paediatric cardiac transplant recipients who had been converted from the oil-based formulation to the micro-emulsified formulation was performed. No clinical rejection episodes occurred following conversion. There was a significant reduction in dose following conversion (p < 0.001). The mean trough level was less on the new formulation (p = 0.04), but there was no difference in coefficient of variation or standard deviation. Mean glomerular filtration rate (GFR) was significantly less, but there was no difference in the rate of change of GFR on the new formulation. Erratic absorption and deteriorating renal function remain as significant problems in paediatric cardiac transplant recipients despite conversion to the new formulation.