A prospective study to investigate the source of pathogenic organisms responsible for infective complications of patients undergoing major oesophageal surgery was undertaken in 138 consecutive patients (38 female and 100 male) with obstructive lesions of the oesophagus, aged 24 to 86 years (mean 67 years). In all patients, the upper alimentary tract (UAT) was opened as part of the surgical procedure and 20.3% had pathogens present in their sputum before surgery. On direct culture of the contents of stomach or oesophagus at operation, 61% showed pathogenic organisms. Twenty-five patients suffered from 28 infections, predominantly pleuropulmonary infection (n = 19) but also wound sepsis (n = 8) and generalised infection (n = 1). Pathogenic organisms could not be cultured from the tracheobronchial tree immediately postoperatively. There was no correlation between preoperative sputum microbiology and postoperative infection. There was, however, a definite correlation (66% of cases) between pathogens of UAT content collected at operation and those responsible for postoperative infection. We conclude that it is relevant and important to regularly obtain samples of UAT content at operation to plan antibiotic regimes.