Cystic fibrosis (CF) is caused by abnormal function of the CF transmembrane conductance regulator (CFTR) gene. CF is highly variable with some individuals succumbing to the disease in their first decade while others live into their fourth and fifth decades. Patients also differ in the involvement of organ systems and in complications. Some of the variation in CF phenotype can be attributed to the nature of the defect in the CFTR gene. The CFTR genotype primarily determines the degree of pancreatic exocrine dysfunction and correlates with a degree of abnormality in the sweat chloride concentration and malformation of the male reproductive tract. However, factors independent of CFTR are responsible for variation in lung disease, the primary cause of morbidity and mortality in CF. Over the past few years, modifier genes have been identified that influence lung disease severity in CF patients. Non-genetic factors such as socioeconomic status and exposure to passive smoking also affect pulmonary outcome. A more complete understanding of the causes of variation among CF patients is emerging, facilitating the development of new prognostic measures as well as novel therapies.