Objective To explore effects of heroin and ephedrine on the histological structure and ChAT activity of hypothalamus and hippocampus of filial mice. Expression of Bcl-2 associated X protein(Bax protein) and keratinocyte growth factor(KGF) of hypothalamus and hippocampus were measured. Methods One hundred and eight filial mice were given intraperitoneal injection of heroin and ephedrine by gradually increase of doses, apoptosis and expression of Bax protein and KGF of hypothalamus and hippocampus were observed by Giemsa staining and immunohistochemistry, and the ChAT activity was detected by colorimetry. Results After administration of heroin and ephedrine at 5,10,15,20 days, the number of apoptotic cells and expression of Bax protein and KGF of hypothalamus and hippocampus were significantly increased and ChAT activity was lower than those of the control group(P<0.05 or P<0.01). There were differences between heroin group and the ephedrine group in the above-mentioned four indexes (P<0.05 or P<0.01). The number of apoptotic cells and Bax protein and KGF immunopositive neurons of hypothalamus and hippocampus increased by the increase in dose of heroin and ephedrine. Conclusions Heroin and ephedrine had great effect on the histological structure and ChAT activity of hypothalamus and hippocampus of filial mice, and this effects would be related to the cell apoptosis of hypothalamus and hippocampus.