Abstract: Objective: To provide anatomical basis for stereotaxis technique through three dimensional reconstruction of amydaloid nuclei with computer. Methods: 20 whole brains were serially horizontally sliced with each Section 2mm in thickness and then amydaloid was reconstructed with these sections images by surface methods. Results: The reconstructed amydaloid nuclei are smooth, nature and realistic. They could be rotated, zoomed and cut in any direction. Conclusion: The three dimensional form and position of the reconstructed amydaloid nuclei have reference value to the stereotaxis technique of encephalon.