Background: There are few data with respect to prothrombotic risk factors in neonates. Aim: To determine the associated risk factors, clinical features and outcome in newborn infants diagnosed with thrombo-embolism. Methods: Case records of 25 infants (17 full-term and eight preterm) diagnosed with thrombo-embolism between January 2005 and April 2008 in a neonatal intensive care unit were reviewed. Results: Of the 25 infants, 18 cases of venous (72%) and seven of arterial (28%) thrombo-embolism were recorded; in 18 it was associated with central catherisation. The sites of thrombosis were portal vein (15), right renal vein (one), right femoral vein (one), multiple veins (one), right femoral artery (3), right iliac artery (2), bilateral iliac and renal arteries (one) and left renal artery (one). Hereditary thrombotic mutations were detected in three patients and anticardiolipin antibody was detected in one, none of whom had been catheterised. The remaining three non-catheterised patients had perinatal risk factors. Venous catheter placement was undertaken in 12 patients (48%), eleven of whom had: umbilical venous catheterisation for exchange transfusion (9), partial exchange transfusion (one) and venous access (one), and one had femoral venous catheterisation for an angiographic study. Arterial catheterisation was undertaken in seven patients (28%) (one infant had both umbilical venous and arterial catheters) for angiographic studies (5) and blood sampling (2). Of the 18 catheterised patients (72%), thrombophilic studies were undertaken in 13 and none had abnormal results. Additional perinatal risk factors were present in 18 patients (72%) and included prematurity (8), congenital heart disease (8), septicaemia (5), dehydration (3), respiratory distress syndrome (3), polycythemia (2), meconium aspiration syndrome (one), pneumonia (one), maternal diabetes (one), necrotising enterocolitis (one) and perinatal asphyxia (one). Although most of the patients recovered after anticoagulant or fibrinolytic therapy, the five (20%) deaths were associated mainly with underlying diseases. Conclusion: The most important risk factor for thrombo-embolic events in neonates is placement of central catheters and some perinatal prothrombotic conditions. Nevertheless, hereditary or acquired thrombophilic risk factors may also be a cause of thrombo-embolism © 2009 The Liverpool School of Tropical Medicine.