Single murine and human intestinal stem cells can be expanded in culture over long time periods as genetically and phenotypically stable epithelial organoids. Increased cAMP levels induce rapid swelling of such organoids by opening the cystic fibrosis transmembrane conductor receptor (CFTR). This response is lost in organoids derived from cystic fibrosis (CF) patients. Here we use the CRISPR/Cas9 genome editing system to correct the CFTR locus by homologous recombination in cultured intestinal stem cells of CF patients. The corrected allele is expressed and fully functional as measured in clonally expanded organoids. This study provides proof of concept for gene correction by homologous recombination in primary adult stem cells derived from patients with a single-gene hereditary defect. Display omitted •The CRISPR/Cas9 system enables genome editing in intestinal stem cell organoids•cAMP-induced swelling is lost in CFTR mutant organoids of cystic fibrosis patients•CRISPR/Cas9-mediated repair of the CFTR locus restores organoid swelling Correction of a disease-causing CFTR mutation in cultured intestinal stem cells from cystic fibrosis patients is demonstrated using the CRISPR/Cas9 system.