Somatosensation is divided into cutaneous sensation such as tactile, pain and temperature sensation and proprioception. Dorsal root ganglion (DRG) neurons project to the peripheral targets including muscles and skin, and centrally to the spinal cord. Subpopulations of DRG neurons which innervate muscle spindles and Golgi tendon organs are called proprioceptive neurons. Proprioceptive neurons play a role in transmitting the proprioceptive information to the central nervous system. In the previous studies, we reported that Runx3 is expressed in the proprioceptive neurons and that projections of these neurons were defective in Runx3-deficient (Runx3-/-) mouse embryos. Although it's highly likely that Runx3 contributes to the axonal projection of proprioceptive neurons, the mechanisms accounting for this phenomenon are unknown. In the present study, we aim to identify axonal guidance-related genes to regulate the axonal projection of proprioceptive neurons in the downstream of Runx3. We performed the micro-array analyses using mRNAs isolated from wild type (WT) and Runx3-/- DRG neurons of embryonic day 12.5 (E12.5). We found that in Runx3-/- DRG neurons, expression levels of Ntrk3 variant 1 (Ntrk3-v1) and variant 2 (Ntrk3-v2) mRNAs, whose transcripts are full-length and truncated TrkCreceptors of neurotrophin-3 (NT3) respectively, decreased significantly as compared with those of WT at E13.5 and E14.5. Furthermore, our data showed that the decreasing rate of Ntrk3-v1 mRNA in Runx3-/- DRG neurons was different from that of Ntrk3-v2 mRNA during development. In addition, from collagen-gel cultures of DRG explants with NT3-soaked beads, we found that the response of E14.5 Runx3-/- DRG neurites to chemoattractive effects of NT3 decreased significantly compared with that of WT DRG neurites. These results suggest that Ntrk3-v1 and Ntrk3-v2 may work as downstream factors of Runx3.