Vancomycin is administered as both prophylaxis and treatment in neonates receiving extracorporeal membrane oxygenation (ECMO), typically after surgery. An open-label, retrospective study was conducted to determine dosing strategies in all neonates who received vancomycin during ECMO and compare pharmacokinetic values with those of matched controls not receiving ECMO. Fifteen neonates receiving ECMO were given vancomycin infused into the circuit, with dosages based on weight and gestational age. Blood for serum concentrations was drawn around the third dose, for trough concentrations immediately before the dose, and for peak concentrations 1 hour after infusion. Samples were analyzed by fluorescence polarization immunoassay. The most frequent regimen for both groups (8 ECMO, 13 controls) was 10 mg/kg every 8 hours. It produced peak and trough concentrations of 27.5 +/- 4.3 and 13.7 +/- 2.7 microg/ml, and 23.0 +/- 5.4 and 13.2 +/- 4.5 microg/ml, respectively. Pharmacokinetic analysis using a one-compartment model revealed volume of distribution of 0.45 +/- 0.18 L/kg, half-life of 8.29 +/- 2.23 hours, and total body clearance of 0.65 +/- 0.28 ml/min/kg in ECMO recipients. Volume of distribution and clearance were not significantly different in controls (0.39 +/- 0.12 L/kg, 0.79 +/- 0.41 ml/min/kg), but half-life was shorter (6.53 +/- 2.05 hrs, p = 0.02). Based on long volume of distribution in neonates receiving ECMO, we recommend that empiric vancomycin regimens incorporate a longer dosing interval than the 6-8 hours commonly recommended for term infants. The effects of severity of illness on drug elimination require additional study.