Objective To examine the three dimensional shape and position relation of the hypothalamus and the pituitary in a 14.5 embryonic day rat by using true color reconstruction. Methods After obtaining the image database of serial sections of a rat embryo and mixing color channels with luminance channel in the software, we observed the reconstruction result of the region of hypothalamus and pituitary. Results The structure position relation in this region was freely observed in the true color reconstruction result due to the real HE stain color and transparence of no tissue region. Conclusion For the structures with complicated spatial position, the true color volume rendering may faciliate the recognization and be consistent with the observing custom.