The fluorescent dye Fast Blue was injected in anaesthetized rats into either skin, muscle or knee joint of the hindlimb. Following retrograde transport of the dye to lumbar dorsal root ganglia, the cell bodies of primary afferent neurons innervating these different target tissues were identified in ganglion sections by fluorescence microscopy. The sections were processed to demonstrate activity of the enzyme thiamine monophosphatase, or immunoreactivity to calcitonin gene-related peptide, substance P, or somatostatin, in Fast Blue labelled neurons. In all cases immunoreactivity to the antineurofilament antibody RT97 was used to classify dorsal root ganglion cells as being either small dark (RT97 negative, unmyelinated axons) or large light (RT97 positive, myelinated axons). The proportion of small dark cells labelled from each target decreased in the order: skin, muscle, joint. Thiamine monophosphatase and somatostatin were present only in small dark cells, while calcitonin gene-related peptide and substance P were found in both small dark and large light cells. In large light cells of all three targets, more contained calcitonin gene-related peptide than substance P. Among small dark cells, thiamine monophosphatase and somatostatin were found predominantly in skin afferents, while calcitonin gene-related peptide and substance P were more common in muscle and joint afferents. The chemical expression of primary afferents is therefore characteristic of the peripheral target they innervate. This could reflect either a maintained influence of the target on the afferents, or the factors which operate only during development.