Lung epithelial structure is altered in asthma, however the precise mechanisms underlying epithelial repair, including differentiation from basal to columnar epithelial cells, are not well defined. In the course of random sequencing of a cDNA library from human lung biopsies, we have identified a novel gene, Ciliated Bronchial Epithelium 1 (CBE1). Expression of CBE1 was induced during in vitro differentiation of bronchial epithelial cells. Synchronous expression with tektin and FOXJ1, downregulation by IL-13 and its tissue distribution strongly suggested that CBE1 is associated with ciliated cells. Two isoforms of the 0.7-kb full-length cDNA were identified, resulting in open reading frames with different carboxyl termini, with no homology to known proteins. Expression of CBE1 in ciliated epithelial cells was confirmed by immunohistochemistry. Quantitative RT-PCR analysis using bronchial biopsies showed no difference of expression of CBE1 between normal and asthmatic subjects. Expression studies showed that CBE1 is nuclear or perinuclear localized, depending on cell type. Regulated expression during differentiation and the sub-cellular localization of CBE1 suggest that it may play an important role in the differentiation and/or function of ciliated cells in human airways.