Dendritic cells (DC) are antigen-presenting cells that activate naive T cells. Murine DC are a heterogeneous population and can be subdivided into distinct subsets with different immune regulatory functions, namely the conventional DC (cDC), which include the CD8(+)Sirpalpha(-) and CD8(-)Sirpalpha(+) DC, and the plasmacytoid DC (pDC). In this study, the phenotype and function of DC subsets in both the thymus and spleen were compared. Significant differences between the thymic and splenic DC were observed in the expression of genes encoding chemokine receptors (CCRs), toll-like receptors (TLRs) and chemokines. Thymic DC expressed high levels of genes encoding a unique set of chemokines (CCL17 and CCL22) known to be important for T-cell development. Moreover, the capacity of the DC from the two organs to produce IL-6, IFN-alpha and IL-12p70 in response to the TLR 9 agonist CpG differed markedly, indicating intrinsic functional differences between subsets with similar surface phenotype. These results indicate that the microenvironment is an important factor that contributes to the functional specification of DC subsets in different lymphoid tissues.