The clinical course of a term neonate (birthweight 3.14 kg) who developed thrombosis of the left common and internal iliac veins on day 21 following recovery from Streptococcus mitis septicemia, with shock diagnosed on day 13, is reported. Subcutaneous low molecular weight heparin (LMWH) was commenced (1.5 mg/kg 12 hourly for 10 days) after 13 h of standard heparin infusion, due to difficulties in securing a peripheral venous access. The inflammation of the left leg was completely resolved by day 5 of LMWH therapy. Prothrombin time, activated prothrombin time and fibrinogen levels were within normal limits during LMWH therapy. Treatment-related side effects, such as thrombocytopenia and bleeding tendency were not noted. Doppler studies 6 weeks after discharge home on day 33 revealed complete resolution of the thrombus. Apart from septicaemia and shock, the presence of an indwelling central venous catheter and a history of untreated maternal diabetes were additional risk factors for thrombosis. Because it is as effective as standard heparin, LMWH may be a therapeutic option for thrombosis in high-risk neonates, particularly given its ease of administration by the subcutaneous route, predictable pharmacokinetics and reduced incidence of adverse effects such as bleeding complications.