Although meconium ileus (MI) is the earliest manifestation of cystic fibrosis (CF), and is associated with poorer growth, the longitudinal pulmonary progression of CF children with MI is not clear. To test the hypothesis that MI is associated with worse pulmonary outcomes, we prospectively compared from diagnosis to 12 years of age 32 CF children with MI to 50 CF children without MI who were diagnosed during early infancy through neonatal screening. Pulmonary outcome measures included respiratory symptoms, respiratory infections, pathogens, antibiotic usage, hospitalizations, quantitative chest radiology, spirometry, and lung volume determinations. Obstructive lung disease was defined as percent predicted spirometry values below the lower limits of normal. Longitudinal analyses revealed no significant differences in cough, wheezing, respiratory infections, prevalence of and median times to acquisition of Pseudomonas aeruginosa or Staphylococcus aureus, antibiotic usage, and chest radiograph scores between the two groups. However, MI children showed significantly worse forced expiratory volume in 1 sec (FEV₁), forced vital capacity (FVC), forced expiratory flow between 25–75% of FVC (FEF_25–75), % predicted FEV₁, % predicted FEF_25–75, and total lung capacity (TLC). These differences were particularly apparent beginning at age 8–10 years. MI children also had higher rates of and shorter median times to obstructive lung disease. Subgroup analyses showed MI children treated surgically and those treated medically had similar pulmonary outcomes. In conclusion, MI children have worse lung function and more obstructive lung disease than those without MI. Such abnormalities are accompanied by reduced lung volume. MI is a distinct CF phenotype with more severe pulmonary dysfunction. Pediatr Pulmonol. 2004; 38:277–284. © 2004 Wiley‐Liss, Inc.