A novel cDNA of human nasopharyngeal epithelium was cloned. The cDNA fragment of the gene, termed NESG1, was originally isolated by mRNA differential display, and was not homologous to any of the known genes in the database. The complete sequence of NESG1 cDNA, 1850 bp, contains an open reading frame of 1575 nucleotides, and encodes a soluble basic protein of 386 amino acids containing multiple protein kinase phosphorylation sites. The deduced protein has no homology to any of the known proteins in the database. A homologous STS localized NESG1 to the chromosomal region of 1q22-24. Messenger RNA of this gene was expressed only in nasopharynx and trachea. These results suggest that the human NESG1 gene may be a specific gene of columnar ciliated epithelium.