Twenty-seven children with complex congenital heart malformations necessitating early repair were studied before and after deep hypothermic procedures. The children were allocated into two groups. One group underwent total circulatory arrest (40 +/- 6 minutes). In the other group perfusion was maintained during deep hypothermia but reduced a 25% of normal at normothermia. The temperature was reduced to 15 degrees C (nasopharynx) in both groups with a combination of topical and core cooling. To study cerebral injury, were made serial measurements of creatine kinase isoenzyme BB from arterial samples before and for 8 hours after the deep hypothermic procedure. Creatine kinase isoenzyme BB increased after both procedures from 4.3 +/- 0.9 ng/ml to 10.4 +/- 1.8 ng/ml in the circulatory arrest group and from 2.8 +/- 0.7 ng/ml to 9.9 +/- 1.9 ng/ml in the low-flow group (no significant difference). The results were analyzed in relation to age, size, study group, hemoglobin, blood glucose, and blood gases. The creatine kinase BB levels were positively related to preoperative hemoglobin and blood glucose values before the hypothermic procedures.