A comprehensive approach to the study of mannose receptor (MR) biology has unveiled an unexpected level of complexity and stresses the importance of post-translational modifications and gene regulation in the analysis of protein function. The existence of endogenous tissue ligands for the MR highlights the need to reduce MR expression in antigen presenting cells and/or to regulate T cell stimulation after presentation of MR ligands, in order to avoid autoimmunity. This regulation might be achieved by down modulation of the antigen presenting cell stimulatory capacity upon MR ligation. In macrophages there are conflicting evidence regarding the outcome of MR recognition. These results are not unexpected if endogenous mannosylated and sulphated self-antigens, that need to be shielded from the immune system, are being eliminated through this receptor. The presence of counter receptors for the cysteine rich (CR) domain of the MR in specialized myeloid cells in lymphoid organs adds a new dimension to this system. It opens the possibility for a delivery pathway for MR carbohydrate recognition domains (CRDs) ligands that needs to be investigated further.