Inflammation is a natural part of wound healing but it can also cause secondary (bystander) damage and/or negatively interfere with endogenous repair mechanisms if non-resolving. Regulation of inflammation is traditionally looked at from the perspective of danger signals, cytokines and chemokines, and their respective receptors. A neuronal contribution to the regulation of inflammation is, however, increasingly appreciated, and this has important implications for the bodily response under conditions where the nervous system itself may be damaged. In this review article, we provide an up-to-date overview of the current literature on neural innervation of primary and secondary lymphoid organs, focusing in particular on the bone marrow and spleen, its significance in relation to immune function and, lastly, also briefly discussing how a major neurotraumatic event like spinal cord injury (SCI) may impact on this.