Serial cultures of endotracheal tube aspirates were carried out in 94 neonates who were intubated and had been ventilated for longer than one week. A similar change in bacterial colonisation with duration of ventilation was seen in infants who subsequently developed sepsis and those who did not. In both groups, 177 aspirates (more than 90%) obtained during the first week of ventilation were sterile. Thereafter, colonisation with mixed Gram positive flora emerged followed by growth of Gram negative bacilli. For the infants who developed sepsis, the correlation between pathogens isolated from blood during the episodes of sepsis and those from previous endotracheal tube isolates was poor; in only five of the 26 cases of sepsis (19%) was the same single strain of organism isolated from culture of the blood and of the endotracheal tube aspirate. Other markers of infection such as endotracheal tube aspirate white blood cell counts and changes in bacterial flora were not useful in predicting systemic infection. Routine surveillance cultures of endotracheal tube aspirates in ventilated infants are not helpful in predicting the pathogens that are isolated from the blood during episodes of sepsis.