Respiratory morbidity and mortality during infancy are important problems in the care of CF patients whether they are diagnosed conventionally or through newborn screening. Although the mechanisms of lung disease in CF remain to be elucidated, two potential pathophysiologic mechanisms--viral infection and undernutrition--can be associated with respiratory morbidity in infancy. Colonization of some infants with Pseudomonas and the presence of early mucus casts and cytokines in bronchoalveolar lavage suggest that pathophysiologic processes that are important in later life may begin in infancy. The early respiratory abnormalities, morbidity and mortality seen in CF indicate the need for future investigations of the respiratory course and interventional trials in infancy.