Abstract: Objective To study whether there is apoptosis in brainstem neurons while aging by oberving the distribution of Caspase-3 positive apoptotic cells in in brainstem of young and old SD rats. Methods Healthy male SD rats were divided into 2 groups (3 and 18 month-old respectively), 3 rats each group. Brainstem specimens were treated followed the brainstem’s common paraffin embedding, sectioning and HE staining procedures (sections were 6 μm in thickness). The sections were also determined by Caspase-3 immunostaining and TUNEL. The Caspase-3 positive cells on the rat stereotaxic atlas were drew, then composed the sections into a 3D model. Results Compared to 3 month-old rats, there were more Caspase-3 positive neurons in the brainstem and the positive neurons were distributed more extensively in 18 month-old rats spectially in nucleus of solitary tract and pontine reticular nuclei. Conclusion More neurons suffer apoptotic changes in the brainstem while aging.