Background &Aims: Cystic fibrosis (CF) is caused by over 1000 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and presents with a widely variable phenotype. Genotype phenotype studies identified CFTR mutations that were associated with pancreatic sufficiency (PS). Residual Cl-channel function was shown for selected PS mutations in heterologous cells. However, the functional consequences of most CFTR mutations in native epithelia are not well established. Methods: To elucidate the relationships between epithelial CFTR function, CFTR genotype, and patient phenotype, we measured cyclic adenosine monophosphate (cAMP)mediated Cl-secretion in rectal biopsy specimens from 45 CF patients who had at least 1 non F508 mutation carrying a wide spectrum of CFTR mutations. We compared CFTR genotypes and clinical manifestations of CF patients who expressed residual CFTR mediated Cl-secretion with patients in whom Cl-secretion was absent. Results: Residual anion secretion was detected in 40%of CF patients, and was associated with later disease onset (P <0.0001), higher frequency of PS (P <0.0001), and less severe lung disease (P <0.05). Clinical outcomes correlated with the magnitude of residual CFTR activity, which was in the range of 12%-54%of controls. Conclusions: Specific CFTR mutations confer residual CFTR function to rectal epithelia, which is related closely to a mild disease phenotype. Quantification of rectal CFTR mediated Cl-secretion may be a sensitive test to predict the prognosis of CF disease and identify CF patients who would benefit from therapeutic strategies that would increase residual CFTR activity. Background & Aims: Cystic fibrosis (CF) is caused by over 1000 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and presents with a widely variable phenotype. Genotype phenotype studies identified CFTR mutations that were associated with pancreatic sufficiency (PS). Residual However, the functional consequences of most CFTR mutations in native epithelia are not well established. Methods: To elucidate the relationships between epithelial CFTR function, CFTR genotype, and patient phenotype, we measured cyclic adenosine monophosphate (cAMP) mediated Cl-secretion in rectal biopsy specimens from 45 CF patients who had at least 1 non F508 mutation carrying a wide spectrum of CFTR mutations. We compared CFTR genotypes and clinical manifestations of CF patients who were residual CFTR mediated Cl-secretion with patients in whom Cl-secretion was absent. Results: Residual anion secret ion was detected in 40% of CF patients, and was associated with later disease onset (P <0.0001), higher frequency of PS (P <0.0001), and less severe lung disease of residual CFTR activity, which was in the range of 12% -54% of controls. Conclusions: Specific CFTR mutations confer residual CFTR function to rectal epithelia, which is related closely to a mild disease phenotype. Quantification of rectal CFTR mediated Cl-secretion may be a sensitive test to predict the prognosis of CF disease and identify CF patients who would benefit from therapeutic strategies that would increase residual CFTR activity.