Sepsis is difficult to identify in patients treated with extracorporeal membrane oxygenation (ECMO). This study evaluates the usefulness of surveillance cultures obtained during ECMO. We retrospectively reviewed the records of 187 patients from four ECMO centers with birth weights 1,574 to 4,900 gm and gestational ages 33-43 weeks, over a 4 year interval. Most patients had surveillance blood cultures daily, and tracheal aspirates and urine culture every other day. Charts were reviewed for culture results before, during, and for the 7 days after ECMO, and clinical response to the culture results. A total of 2,423 cultures were obtained during 1,487 days of ECMO, of which 155 were positive (6.4%): 13 of 1,370 blood cultures (0.9%), 137 of 850 tracheal aspirate cultures (16%), and 5 of 203 urine cultures (2.3%). After 72 hours, tracheal aspirate cultures became positive with nosocomial organisms in 33 of 131 patients. None of 153 bacterial urine cultures were positive, and only one of 34 viral urine cultures were positive (CMV). We conclude that routine daily blood cultures are not useful in neonatal ECMO. Tracheal aspirate cultures may be helpful in the management of antibiotic therapy in patients on ECMO for more than 5 days. Routine bacterial urine cultures did not provide useful information.