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Patients undergoing surgery for congenital heart disease are at high risk for bleeding as well as thrombosis in the postoperative period. The objective of the study was to describe the design and effects of implementing a standardized unfractionated heparin anticoagulation protocol for children after congenital heart surgery.We created a tiered guideline for the postoperative management of bleeding and thrombosis. In patients treated with unfractionated heparin, anti-factor Xa activity level as well as activated partial thromboplastin time were used for dose titration. Clinical outcomes, including bleeding and thrombosis events, were prospectively collected for 5 months before and after protocol implementation and adjudicated as either minor, clinically relevant nonmajor, or major.Among 792 surgical patients followed during the study period, a total of 203 patients (87 preimplementation, 116 postimplementation) were treated with therapeutic unfractionated heparin over a total of 1481 patient days. Of these, 28% were neonates and 35% were infants (29 days to 1 year), with a trend toward fewer neonates and lower Risk Adjustment for Congenital Heart Surgery (RACHS) scores after protocol implementation. Among 1321 time-matched pairs, activated partial thromboplastin time and antifactor Xa activity levels were poorly correlated (r2 = 0.33). Clinically relevant bleeding events, which required increased medical care, including blood transfusion, decreased after protocol implementation (4.14 vs 1.62 bleeding events per 100 patient-days; risk ratio, 0.39 [0.20-0.75]; P = .005), even after correcting for differences in age and RACHS scores (P = .006). This finding was primarily found after RACHS category 1 to 3 procedures (risk ratio, 0.27 [0.10-0.73]; P = .0099) and in noninfants (risk ratio, 0.25 [0.09-0.65]; P = .005). There were no significant differences in the incidences of major bleeding (P = .88) or any thrombosis (P = .55).The use of a standardized anticoagulation protocol is feasible and might reduce the incidence of bleeding and thrombosis events in postcardiotomy patients.