In 2009, the U.S Food and Drug Administration (FDA) announced a two-phase change in unfractionated heparin to reduce contamination and create a new potency reference. The FDA announced the change would bring about a 10% decrease in potency from the old heparin (OH) to new heparin (NH). The purpose of this article is to compare heparin in pediatric patients undergoing cardiac surgery before and after the FDA changes. After Institutional Review Board approval, a retrospective chart review was conducted with pediatric patients (n = 266) undergoing cardiac surgery. All patients received a heparin loading dose of 400 IU/kg and data collected included patient demographics, baseline activated clotting time (ACT), ACT after initial heparin dose, and heparin dose–response. These data were then further broken down into age blocks consisting of neonates (<1 month), 1–12 months, 1–5 years old, and older than 5 years old. In 17.3% of cases in the NH group, the ACT after the initial heparin dose did not reach the critical value of 400 seconds necessary for initiation of cardiopulmonary bypass (CPB). This is significantly higher than the 8.9% of cases in the OH group (p < .05). There was an overall trend among age groups that the NH was less potent than OH. However, only the 1–5 years of age group showed significance at p < .05. Given the median ACTs 591 seconds for OH and 484 seconds for NH, the calculated percentage difference was 18.1%. The results from this retrospective pediatric chart review indicate that the change in heparin potency greatly deviates from the 10% change reported by the FDA. In conclusion, NH has a trend of lower potency and frequent monitoring is necessary to maintain a safe level of anticoagulation during CPB.