To identify the pathogenic micro-organisms that had colonised preoperatively in clefts in the soft palate and oro-nasopharynx, we retrospectively studied the preoperative microbiological profiles of 200 infants who had had primary repair of all types of cleft in the soft palate. Data from a private practice that specialises in the repair of facial clefts were extracted randomly from patients' files. We analysed the results of the culture of preoperative swabs taken from clefts in the soft palate and oro-nasopharynx, and the resistance profile of organisms towards various antibiotics. A total of 23 different pathogenic micro-organisms were isolated from 115 (57%) of the sample. Klebsiella pneumoniae most commonly colonised clefts in the lip, alveolus, and palate. This was considerably higher than in other groups. The second most common micro-organism was Staphylococcus aureus, which was found most often in patients with isolated clefts in the hard palate. Those with complete cleft lip and palate presented with more pathogenic micro-organisms in preoperative cultures than those with other types of cleft. We need to find a way to control pathogenic micro-organisms in the oral and oro-nasopharyngeal region preoperatively to limit postoperative complications.