The Na⁺-H⁺ exchanger regulatory factor (NHE-RF) is a cytoplasmic phosphoprotein that was first found to be involved in protein kinase A mediated regulation of ion transport. NHE-RF contains two distinct protein interaction PDZ domains: NHE-RF-PDZ1 and NHE-RF-PDZ2. However, their binding partners are currently unknown. Because PDZ domains usually bind to specific short linear C-terminal sequences, we have carried out affinity selection of random peptides for specific sequences that interact with the NHE-RF PDZ domains and found that NHE-RF-PDZ1 is capable of binding to the CFTR C-terminus. The specific and tight association suggests a potential regulatory role of NHE-RF in cystic fibrosis transmembrane conductance regulator (CFTR) function.