The lung function of infants with cystic fibrosis is often reduced shortly after diagnosis. We measured the airway function of newly diagnosed infants to test whether this reduction is independent of clinically recognised lower respiratory illness. We compared the airway function of 33 infants with cystic fibrosis and 87 healthy controls after adjustment for sex, age, bodyweight and length, and exposure to maternal smoking. Airway function was significantly reduced in children with cystic fibrosis, even in those without clinically recognised previous lower respiratory illness. Our findings raise important questions about the onset and natural history of impaired airway function in infants with cystic fibrosis.