Previous analysis of CFTR-knockout (CFTR-/-) in piglets has provided important insights into the pathology of cystic fibrosis. However, controversies exist as to the true contribution of CFTR to the pH balance in airways and intestine. We therefore compared ion transport properties in newborn wild-type (CFTR+/+) and CFTR-knockout (CFTR-/- piglets). Tracheas of CFTR-/- piglets demonstrated typical cartilage malformations and muscle cell bundles. CFTR-/- airway epithelial cells showed enhanced lipid peroxidation, suggesting inflammation early in life. CFTR was mainly expressed in airway submucosal glands and was absent in lungs of CFTR-/- piglets, while expression of TMEM16A was uncompromised. mRNA levels for TMEM16A, TMEM16F, and alpha beta gamma ENaC were unchanged in CFTR-/- airways, while mRNA for SLC26A9 appeared reduced. CFTR was undetectable in epithelial cells of CFTR-/- airways and intestine. Small intestinal epithelium of CFTR-/- piglets showed mucus accumulation. Secretion of both electrolytes and mucus was activated by stimulation with prostaglandin E2 and ATP in the intestine of CFTR+/+, but not of CFTR-/- animals. pH was measured inside small bronchi using a pH microelectrode and revealed no difference between CFTR+/+ and CFTR-/- piglets. Intracellular pH in porcine airway epithelial cells revealed only a small contribution of CFTR to bicarbonate secretion, which was absent in cells from CFTR-/- piglets. In contrast to earlier reports, our data suggest a minor impact of CFTR on ASL pH. In contrast, enhanced amiloride-sensitive Na(+)absorption may contribute to lung pathology in CFTR-/- piglets, along with a compromised CFTR- and TMEM16A-dependent Cl(-)transport.