The purpose of this study was to measure the ionized magnesium (iMg) concentrations in children undergoing the correction of congenital heart defects. iMg levels were measured in 115 consecutive patients at five sample periods: prebypass, onset of bypass, during rewarming, immediately postbypass, and 1 h postbypass using an ion-selective electrode of the NOVA-CRT 8 (Nova Biomedical, Watham, MA). The incidence of dysrythmias was noted. Patients were divided into two groups: those who received Plegisol as the cardioplegic solution and those who did not. This study demonstrates that iMg decreases with the onset of cardiopulmonary bypass (CPB) in patients who weigh < 10 kg. In the Plegisol group, all subgroups of patients demonstrated statistically higher iMg during the rewarming phase of CPB, immediately post-CPB, and 1 h post-CPB, when compared with control values. The probability of dysrhythmias in the Plegisol group was almost twice that of the non-Plegisol group. However, this did not reach statistical significance (P = 0.22). The results of our study demonstrate that the use of CPB on pediatric patients produces alterations in the iMg. The changes differ depending on both patient weight and the use of a magnesium-containing cardioplegic solution, exemplified here by Plegisol. The role of these changes in iMg on dysrhythmias could not be further evaluated.