The Cl- transporting proteins CFTR, SLC26A9, and anoctamin (ANO1; ANO6) appear to have more in common than anticipated initially. They all participate in the pathogenic process and clinical outcome of renal and airway diseases. In the present review we will therefore concentrate on recent findings concerning electrolyte transport in airways and kidney, and the role of CFTR, SLC26A9, and anoctamins (ANO1 and ANO6). A particular focus will be on the airway diseases cystic fibrosis and asthma, as well as renal alkalosis and polycystic kidney disease. In essence, latest findings are summarized that demonstrate CFTR as the only relevant secretory Cl- channel in airways under basal (non-stimulated) conditions and after stimulation by secretagogues. For proper CFTR function, expression of ANO1 and ANO6 appears to be a prerequisite. Evidence is summarized suggesting that the Cl- transporter SLC26A9 may have a reabsorptive rather than a Cl- secretory function in the airways. In renal collecting ducts bicarbonate secretion takes place due to synergistic tasks of CFTR and the Cl-/HCO3- transporter SLC26A4 (pendrin), which is likely to be supported by ANO1. Finally, in autosomal dominant polycystic kidney disease (ADPKD), the secretory function of CFTR in renal cyst formation might have been overestimated, while ANO1 as well as ANO6 turned out to be crucial in ADPKD, and therefore represent novel pharmacological targets for the treatment of polycystic kidney disease.