The Clec9A-diphtheria toxin receptor (DTR) transgenic mouse strain provides a robust animal model to study the function of lymphoid organ-resident CD8(+) dendritic cells (DCs) and nonlymphoid organ-specific CD103(+) DCs in infectioous diseases and inflammation. Here we describe some basic protocols for CD8(+)/CD103(+) DC isolation, for their in vivo depletion, and for their characterization by multi-color flow cytometry analysis. As an example for in vivo functional characterization of this DC subset, we present here the experimental cerebral malaria model. Furthermore, we illustrate advantages and pitfalls of the Clec9A-DTR system.