A new link between the genetic defect and lung pathology in cystic fibrosis (CF) has been established by the recent discovery of an abnormally acidic pH in the organelles of CF respiratory epithelial cells, along with an increased acidity of the CF airway surface liquid. The defect in cystic fibrosis transmembrane resistance regulator (CFTR) results in hyperacidification of the trans-Golgi network, an organelle responsible for glycosylation, and protein- and membrane-sorting in mammalian cells. Hyperacidification and altered surface glycoconjugates might contribute to mucus thickening, bacterial adhesion and colonization, inflammation, and irreversible tissue damage. The increased acidity of the intracellular organelles and of the lung lining in CF could be linked, and both represent potential therapeutic targets.