Determine the effect of age and congenital heart disease (CHD) on whole blood tests for monitoring unfractionated heparin (UFH) in children. Determine correlation with anti-Xa levels in children undergoing cardiac catheterization or cardiac surgery. A prospective cross-sectional study of 211 healthy children about to have minor surgery (median age 3.5 years) and 110 CHD patients (median age 2.1 years) undergoing cardiac catheterization or cardiac surgery. Commonly used whole blood tests (two activated clotting times and an activated partial thromboplastin time; ACT+, ACT-LR, and APTT, respectively) were obtained before procedures and after UFH in CHD patients. Data were analyzed for effect of age and CHD and correlation with anti-Xa levels. In healthy subjects the ACT+ was lower in younger (<3 years) patients while the ACT-LR and APTT were unaffected. CHD patients exhibited an opposite trend with higher values in the younger patients. After bolus heparin the ACT+ exhibited the strongest correlation (r = 0.89) with anti-Xa levels in both locations (the APTT was too sensitive at post-bolus levels). When anti-Xa levels were below 1.0 IU/ml (range of thromboembolism therapy 0.35-0.7 IU/ml), the APTT correlation coefficient was 0.72. Some whole blood coagulation tests are affected by age in healthy children similar to laboratory tests and are variably influenced by the presence of CHD. ACT+ is the most reliable predictor of anti-Xa levels in both catheterization and surgery for pediatric patients. The APTT exhibited stronger correlation with anti-Xa than previous reports of laboratory APTT and warrants further evaluation for monitoring heparin thromboembolism therapy.