The aim of this prospective non-interventional investigation was to study whether preoperative colonization of nasopharynx with potentially pathogenic airway bacteria carried an increased risk for the development of early postoperative bacterial airway infections after heart surgery in preschool children. Of the 91 patients studied, 62 (68%) were colonized preoperatively in the nasopharynx with Moraxella catarrhalis, Streptococcus pneumoniae, Haemophilus influenzae and/or Staphylococcus aureus. Nine children developed postoperative airway infections (four pneumonia, three bacterial bronchitis and two acute otitis media). Preoperative colonization was not significantly associated with increased risk for postoperative airway infection: 6/62 (10%) in colonized vs 3/29 (10%) in non-colonized children. Preoperative nasopharynx cultures in asymptomatic children should be avoided since it is unpleasant for the child, is not cost-effective, and may lead to unnecessary antibiotic treatment.