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Objective Complete heart block develops as a result of damage to the cardiac conduction system after 1–3% of open-heart surgeries for congenital heart disease. This study was performed to identify clinical predictors of permanent complete heart block in the immediate post-operative period. Design Retrospective cohort study. Setting Cardiac intensive care unit in two quaternary children's hospitals. Patients From 2004 to 2015, 5480 open-heart surgeries were performed. Seventy-four patients with complete heart block lasting > 6 h were identified. Measurements The status of atrioventricular conduction was evaluated using pacemaker checks and 12-lead electrocardiograms. The patient data collected included gender, type of heart defect and surgery, age and weight at surgery, clinical parameters in the immediate post-operative period, presence of complications, and hospital mortality. Main Results Complete heart block complicated 1.35% of the open-heart surgeries with 58% representing transient block and 42% permanent block. Comparison between these two groups revealed that a longer surgery is a risk factor for permanent complete heart block. The other main risk factor was morbidity in the immediate post-surgical period, including severe hemodynamic compromise, mechanical ventilation longer than 5 days and a cardiac re-intervention within 14 days after surgery. Mortality was also higher in the group with permanent complete heart block. A multivariable logistic regression analysis showed that the significant risk factors for permanent atrioventricular conduction block included a cardiac re-intervention in the first 2 weeks after the initial surgery and the presence of moderate to severe post-operative complications. Conclusions Our study demonstrates that even if the cardiac conduction system suffers acute injury at the time of surgery in children with congenital heart disease and develops post-operative conduction defects, its restitution seems to be intrinsically related to the well-being of the system as a whole during the first 7 to 10 days after surgery.