By expression cloning using FACS, we have isolated cDNA clones encoding human CD34 from a megakaryoblastoid cell line. The predicted amino acid sequence of CD34 revealed the type I transmembrane protein consisted of a leader peptide (31 residues), an extracellular domain (258 residues), a transmembrane domain (23 residues) and a cytoplasmic domain of 73 residues. In addition, a second form of cDNA that has 194 bp insertion in the cytoplasmic region was isolated. The analysis of genomic DNA showed that this sequence is inserted between the predicted transmembrane and cytoplasmic exons due to an alternative usage of an imperfect 5' splice acceptor site in the 5' flanking region of the cytoplasmic exon. The insertion brings a stop codon so that the protein encoded by this type of mRNA has only 16 residues in the cytoplasmic domain. This truncated form of CD34 molecule can be expressed on the cell surface, and its expression seems to change in association with cell differentiation. A search of the National Biomedical Research Foundation Protein Sequence Database (NBRF) with the Predicted amino acid sequence of CD34 did not reveal homology to any known protein. Thus, the CD34 molecule represents a novel type of cell surface molecule that may have a role in early differentiation process of hematopoietic stem cells.