Deletion of phenylalanine at position 508 (delta F508) in the first nucleotide-binding fold of the cystic fibrosis transmembrane conductance regulator (CFTR) is the most common mutation in patients with cystic fibrosis. Although retaining functional Cl- channel activity, this mutant is recognized as abnormal by the cellular “quality control” machinery and is retained within the endoplasmic reticulum (ER). We have used human epithelial cells and recombinant Chinese hamster ovary cells to identify molecular interactions that may contribute to this intracellular retention. Based upon coimmunoprecipitation and cosedimentation through glycerol density gradients, newly synthesized wild-type and delta F508 mutant CFTRs associated specifically with calnexin, the calcium-binding transmembrane chaperone of the ER. This association was restricted to the immature (or ER-associated) forms of the CFTR proteins. Although the bulk of wild-type and delta F508 CFTRs were present initially in complexes containing calnexin, only wild-type CFTR was able to escape from this association and exit the ER. Calnexin retains misfolded or incompletely assembled proteins in the ER and thus is likely to contribute to the mislocalization of mutant CFTR.