Gene expression profiles of hematopoietic stem cells (HSCs) provide clues for understanding molecular mechanisms of HSC behavior, including self-renewal and differentiation. We took advantage of serial analysis of gene expression (SAGE) to identify medium- and low-abundant transcripts expressed in HSCs/hematopoietic progenitor cells (HPCs). Among a total of 31,380 unique transcripts, 17,326 (55%) correspond to known genes and, 14,054 (45%) are low-copy transcripts that have no matches to currently known genes. Among the former class, 3,899 (23%) were alternatively spliced transcripts and 3,754 (22%) represent anti-sense transcripts from known genes. Mapping of the SAGE tags to the mouse genome showed that differences in gene expression exist among chromosomes. In addition, comparison of the HSCs/HPCs SAGE data to that of myeloid progenitor cells revealed that massive genetic reprogramming occurs in hematopoietic cell differentiation. Our results demonstrate a previously unrecognized complexity of gene expression in HSCs/HPCs, and indicate the need for further efforts to fully identify and characterize the transcripts expressed in this cell type.