Six transtracheal aspirations (TTA) and expectorated sputum specimens were collected from four children suffering from cystic fibrosis who had pulmonary infection. Specimens obtained from both sites were cultured for aerobic bacteria and TTA aspirates were also cultured for anaerobes. Differences in bacteria isolated in TTA and sputum aspirates were present in all instances. Six isolates were recovered in both sites (three Pseudomonas aeruginosa, two Staphylococcus aureus and one Aspergillus flavus). Five aerobic isolates were recovered only in the expectorated sputum and not in TTA aspirations (two Klebsiella pneumoniae and one each of P. aeruginosa, Escherichia coli and Proteus mirabilis). Nine organisms were isolated only from the TTA (two each of Veillonella parvula and Alpha hemolytic streptococci, and one each of Bacteroides fragilis, B. melaninogenicus, Lactobacillus sp., Haemophilus influenzae and Gamma hemolytic streptococci). The recovery of anaerobic organisms from four of the six TTA specimens suggests a possible role for these organisms in the etiology of pulmonary infection in cystic fibrosis. We found TTA to be helpful in the bacterial diagnosis and management of pulmonary infections in cystic fibrosis.