Cystic fibrosis (CF) is a multisystem disease causing severe chronic sinopulmonary disease and loss of pancreatic exocrine function, which affects approximately 70,000 individuals worldwide. New therapeutic developments over the last few decades have resulted in a significant increase in survival, with the median predicted survival now reaching the late thirties and more and more CF patients living well into adulthood. However, with this advent of new therapies and the associated increase in survival, new challenges in CF care have also emerged. Two of these challenges, i.e. chronic methicillin-resistant Staphylococcus aureus lung infection and patient adherence to very complicated and time-consuming therapeutic regimens, are reviewed in detail here. In addition, the ultimate challenge of treating the underlying cause of CF by correcting the dysfunction of the CF transmembrane conductance regulator chloride channel is reviewed, as agents to correct channel function will likely significantly alter CF clinical outcomes and treatment approaches in the next decade.