Thrombotic events cause significant morbidity and mortality in children who undergo surgery for complex congenital cardiac disease. We prospectively evaluated the incidence of thrombosis and examined preoperative and postoperative laboratory tests of coagulation and inflammation in neonates experiencing initial surgical palliation for variations of single ventricle physiology. Neonates (<30 days) requiring initial surgical palliation were studied. All subjects received aspirin from postoperative day 1 onward. Thromboses were diagnosed by serial transthoracic echocardiograms, vascular imaging, and interstage cardiac catheterizations according to predefined criteria. Twenty-two neonates, age 1 to 11 days (mean 4 +/- 2.5) were studied. Follow-up ranged from three hours to 18 months (median, 212 days). Eight infants died. Four of the 14 subjects who survived (28%), and one of the eight who died (12.5%), had evidence of thrombosis identified over a range of four hours to nine months postoperatively (median 14 days). When compared with reference values established in healthy children, preoperative subject hematocrit (Hct), platelet count, factors II, V, VII, VIII, and X, antithrombin, protein C, and soluble CD40 ligand measures were significantly lower, and the prothrombin time and partial thromboplastin time were significantly higher. Postoperative C reactive protein (CRP) was significantly higher, and Hct and platelet count significantly lower, than preoperative values. Thrombotic events were significantly related to high preoperative CRP (p = 0.02). Thrombotic complications occur frequently in neonates undergoing initial palliative surgery, suggesting that aspirin therapy alone may constitute inadequate protection. Elevated preoperative CRP appears to be associated with increased thrombotic risk.