The anticoagulation treatment of children on pulsatile assist devices was studied. The results of 40 children (group A) on mechanical circulatory support with the formerly used anticoagulation treatment were compared with 32 children (group B) on assist devices treated with a new anticoagulation regime. In groups A and B, respectively, 19 (47.5%) and 12 (38%) had bleeding complications; 14 (35%) and 8 (25%) had chest re-exploration; 2 (5%) and 1 (3%) had cerebral hemorrhage; 9 (23%) and 7 patients (22%) had thromboembolic events; and 6 (15%) and 2 (6%) had strokes. In groups A and B, respectively, mean time of support was 19 days (range, 0 to 111 days) and 57 days (range, 1 to 420 days), with long-term survival of 33% and 78%. The differences in survival were significant (alpha = 0.003). Embolic and bleeding complications were seen in both groups, but the incidence was lower in group B. Since, however, thrombogenicity of the systems continues to be their main problem, further improvement of treatment is required.