The immune and nervous systems communicate through an array of signalling molecules which includes substance P. This work investigates the anatomical relationship between substance P nerve fibers, receptors, and substance P positive cells in the thymus. Thymuses from rats were frozen or paraformaldehyde fixed. In vitro autoradiography was used to map the distribution of SP receptors. Immunostaining was used to localize SP positive cells and nerve fibers by transmitted light and confocal microscopy. SP receptors exhibited a broader distribution than previously reported, being present throughout the organ with a preferential concentration in the cortico-medullary zone. While SP fibers were frequently associated with the blood vasculature, they were also present throughout the organ independent of blood vessels and were most prominent in the cortico-medullary zone. SP positive cells followed a similar pattern of distribution as the SP fibers and were present as single cells or aggregates of SP positive cells. Confocal microscopy revealed close spatial contact between the SP positive nerve fibers and the SP positive thymic cells. The close spatial relationship between the SP positive thymic cells and SP positive nerve fibers supports the concept of a structural-functional unit between SP nerve fibers and their potential receptor-bearing target cells in the thymus.