Objective To detect the serum level of glycogen phosphorylase isozyme BB (GPBB) in infants of diabetic mothers (IDMs) with myocardial damage and discuss its clinical significance. Methods Totally 132 IDMs who were admitted to the Neonatal Ward in the Affiliated Hospital of Hebei University from January to December 2014 were selected as the study subjects. Their blood GPBB level was detected at 3, 6, 12 and 24 h after birth, and compared with the control group. Of the 132 IDMs, 40 were diagnosed as myocardial damage (myocardial damage group) and 92 did not have myocardial damage (non-myocardial damage group). And the GPBB levels were compared among myocardial damage group, non-myocardial damage group and control group at each time point. The correlations between GPBB level and the perinatal risk factors were also discussed. Rusults The GPBB level of the myocardial damage group was higher than those of the non-myocardial damage group and the control group at 3, 6, 12 and 24 h after birth (P < 0.05). GPBB level was greatly affected by poor control of serum glucose in the mothers during pregnancy, long course of gestational diabetes ( ≥ 3 months), and neonatal hypoglycemia (P < 0.05). Conclusions GPBB could be used as an early sensitive marker of myocardial damage in IDMs.