Objectives Ischemia-modified albumin (IMA) is a new biochemical marker of ischemia. We aimed to search blood IMA levels in neonates with congenital heart defects. Study Design During the study period, patients diagnosed with congenital heart disease and newborns with a diagnosis of hyperbilirubinemia as a control group were included in the study. IMA level was analyzed using the IMA absorbance unit (ABSU) method. Results In total, 57 newborns with congenital heart disease requiring cardiac operation for the study group and 38 newborns for the control group were included. There was no difference between the two groups in terms of gender, mode of delivery, and weeks of gestation. The average IMA values in the control group were 0.19 ± 0.09 ABSU. The prepostoperative mean IMA values of the patient group were 0.22 ± 0.07 and 0.23 ± 0.07 ABSU, respectively. Comparison of the postoperative IMA with the mean of the control group was statistically significant. Preoperative and postoperative IMA values of patients who have died due to primary heart disease and surgical complications were 0.21 ± 0.07 (0.08–0.32) ABSU and 0.25 ± 0.06 (0.12–0.36) ABSU, respectively. IMA levels were not statistically different between the two groups. Conclusion Hypoxia and ischemia in congenital heart disease in the newborn period both preoperatively and postoperatively were important in prognosis. IMA was higher in the postoperative group. Many comprehensive studies are important in terms of preventing complications and decreasing mortality and morbidity by commenting on prognosis. Key Points