Even in patients with cystic fibrosis (CF) with identical CFTR genotypes, there is a wide range in the severity of lung disease, with some individuals facing death or lung transplantation early in life and others demonstrating mild lung disease well into adulthood. Although numerous environmental factors have been identified that influence CF pulmonary phenotype, there is now growing evidence that polymorphic variants in genes besides CFTR play an important role in determining severity of CF lung disease. This article reviews the most recent findings regarding genetic modifiers in CF and also discusses in detail the strategies currently being used to identify novel modifiers of CF pulmonary phenotype. These include single- and multicenter studies, twin and sib studies, microarray approaches, and whole genome association studies.