Inflammation and oxidative damage are believed to play an important role in the postoperative complications after cardiopulmonary bypass (CPB) in neonates. During the preparation of the prime, red blood cells (RBCs) release non-protein-bound iron (NPBI) and free haemoglobin/haem (Hb/haem). The presence of these prooxidants in the prime solution may increase oxidative stress in neonates undergoing CPB. The solution used as the basis of the prime solution may influence the degree of this oxidative stress. We investigated the NPBI and the Hb/haem binding capacities of two different prime solutions: a prime based on pasteurized human albumin and a prime based on fresh frozen plasma. The presence of NPBI and free Hb/haem were measured during and after the preparation of the prime solution. Only in the albumin prime was NPBI detectable. However, in both primes, the concentrations of free Hb/haem increased. Thus, to reduce the prooxidative effects of NPBI and free Hb/haem, RBCs should be added to the prime at the last possible moment. Adding fresh frozen plasma should be considered, as this would result in no detectable NPBI in the prime solution.