Dendritic cells (DC) are professional antigen presenting cells that play a pivotal role in initiating primary immune responses and have been implicated in determining the balance between immunity and tolerance. DC originate from hematopoietic stem cells in bone marrow and different DC subsets have been identified according to their phenotype, function, activation state and location. Gene expression analysis of DC by DNA microarrays represents a systemic approach to the underlying complexity of DC biology and is expected to provide important clues to the application of DC in the clinic. Here we review the recent findings from the use of DNA microarrays in DC biology and discuss the challenges emerging from these studies.