The development of dendritic cells (DCs) from hematopoietic progenitors is not well understood. Using a spleen-derived long-term culture (LTC) system, it has been possible to continuously generate DCs from progenitors maintained in culture. The nonadherent LTC-DC population is composed of 2 major subsets. These are the small LTC-DC or DC precursors and their progeny, the large LTC-DCs that phenotypically resemble immature DCs. In this study, subtracted cDNA libraries were generated containing sequences differentially expressed in small or large LTC-DCs. Differential screening was then used on plated library clones to select genes expressed in either the small or the large cell population. Real-time polymerase chain reaction (PCR) has been used to verify the selection procedure for several genes of particular interest. Known genes isolated from subtracted libraries were related to stages in DC development and supported previous findings regarding the function of small and large LTC-DCs. Large LTC-DCs expressed a number of immunologically important genes encoding CD86, CCR1, osteopontin, and lysozyme. Small LTC-DCs resembled progenitor DCs expressing genes related to the organization of the cytoskeleton, the regulation of antigen processing, and a number of mitochondrial and ribosomal proteins. Novel transcripts were isolated from small and large LTC-DC-subtracted libraries that could encode novel proteins important in DC development. this study describes changes in gene expression related to the development of CD11c(+)CD11b(+) major histocompatibility complex 2 low (MlHC2(lo)) CD8alpha(-) DCs from precursors in a stroma-dependent culture system in the absence of exogenous cytokines.