Abstract: Objective To test the compatibility of Fluoro-Gold(FG) and Fluoro-Ruby(FR) with tissue clearing technique(3 DISCO)and complete stereoscopic imaging. Methods The compatibility of FG and FR with a tissue clearing technique(3 DISCO) was evaluated by slice experiments. After labeling brain and spinal cord with FG and FR, the three dimensional imaging of labelled conduction bundle was shown by optical equipment and transparent to the whole brain and spinal cord of rats. Results Fluorescence signal of Fluoro-Gold and Fluoro-Ruby after 3 DISCO transparency did not attenuate, and could fulfill the requirements of scientific research. After transparent to the brain and spinal cord of rats, FG resulted in strong retrograde labelling of the neurons and dendrites,while FR resulted in strong retrograde labelling of the long-distance axons under two-photon microscope. Conclusion FluoroGold and Fluoro-Ruby have good compatibility with 3 DISCO. The stereoscopic imaging of tissue can be constructed through the combination of tissue optical clearing techniques and optical equipment.