The objective of this paper is to explore the effect of chronic hypoxic hypercapnia on the apoptosis of rat neural cells in the hippocampus, as well as the relationship between apoptosis and Bcl-2 and Bax gene expression. In this study, 50 male Sprague-Dawley rats were randomly divided into 5 groups: a normal control group, and 4 hypoxic hypercapnia groups which received hypoxic hypercapnia treatment for 1, 2 , 3 and 4 weeks. The in situ apoptosis in the hippocampus was detected by TUNEL staining. The expression of bcl-2 and bax mRNA in the hippocampus was examined by RT-PCR. Results showed that the apoptosis index (AI) and expression of Bax mRNA increased with the duration of hypoxic hypercapnia, and that the expression of Bcl-2 mRNA increased at the beginning but then declined. There was a significant positive correlation between AI and the expression of Bax mRNA (r = 0.814, p < 0.01), and there was a significant negative correlation between AI and the ratio of Bcl-2 mRNA/Bax mRNA (r = –0.405, p < 0.01). The results suggest that apoptosis can be induced by chronic hypoxic hypercapnia in the rat hippocampus. The ratio of Bcl-2/Bax declined gradually, which accelerates the occurrence of apoptosis.