To evaluate the significance of early bacteriologic findings in infants and younger children with cystic fibrosis, we divided patients identified at < or = 2 years of age into groups by initial oropharyngeal culture: group NF, normal respiratory flora (n = 17); group SA, Staphylococcus aureus without Pseudomonas aeruginosa (n = 20); group PA, P. aeruginosa without S. aureus (n = 6); group PA/SA, P. aeruginosa and S. aureus (n = 7); and group O, other potentially pathogenic bacteria (n = 31). Follow-up of patients ranged in age from 5.4 to 13 years. At diagnosis, group PA/SA had lower Brasfield scores (p < 0.02) and higher gamma-globulin levels (p < 0.03) than the other groups. Five years after diagnosis, Brasfield scores were significantly lower in groups PA and PA/SA compared with the other groups; mean gamma-globulin levels did not differ significantly among the groups. Groups PA and PA/SA also had evidence of significantly greater obstructive pulmonary disease by spirometry than groups NF and O. Group PA/SA had a 10-year survival estimate of 57%, significantly lower than the 92% to 100% estimates of the other four groups (p < 0.0001). Thus P. aeruginosa in initial oropharyngeal cultures from patients < or = 2 years of age with cystic fibrosis was associated with significantly increased morbidity, and the finding of P. aeruginosa and S. aureus together in initial oropharyngeal cultures with a significantly increased mortality rate during the first 10 years after diagnosis.