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Members of the family of calcium-activated chloride channels (CLCA) have been implicated as modulators of the phenotype in cystic fibrosis (CF). Here, the expression levels of the murine mCLCA1, mCLCA2, mCLCA3 and mCLCA4 were quantified by real-time RT-PCR in the small intestines of CF (cftr (tm1Cam), cftr (TgH(neoim)1Hgu)) and wild type C57BL/6, BALB/c, DBA/2 and NMRI mice. Markedly different expression levels of all four CLCA homologs were observed between the different wild type strains. Expression of mCLCA1 and mCLCA4 was similar in CF versus wild type. In contrast, mCLCA3 mRNA copy numbers were increased up to threefold in all CF models. Immunohistochemical detection of mCLCA3 and PAS reactions on consecutive tissue sections identified a similar increase in mCLCA3 expressing goblet cells, suggesting that elevated mRNA copy numbers of mCLCA3 are due to goblet cell hyperplasia rather than transcriptional regulatory events. Increased mCLCA2 mRNA copy numbers, however, were considered more likely to be due to transcriptional upregulation. Changes in mRNA copy numbers were not associated with altered cell kinetics as determined by immunohistochemistry using antibodies to phospho-histone 3 and activated caspase-3. The results suggest that both mCLCA2 and mCLCA3 may act as modifiers of the intestinal phenotype in CF.