Amyloid-β (Aβ) plays a causative role in Alzheimer's disease. Apolipoprotein E (apoE) is involved in Aβ accumulation, whereas occlusal disharmony increases Aβ production in the rat hippocampus. The purpose of the present study was to investigate the effects of apoE deficiency and occlusal disharmony on Aβ production and spatial memory. Wild-type (WT) (n = 12) and apoE-deficient [ApoE(-/-)] (n = 12) rats (Sprague-Dawley; 8 weeks old) were used. These rats were randomly divided into four groups of six rats each: two control (C) groups: WT (C-WT) and ApoE [C-ApoE(-/-)], and two occlusal disharmony (D) groups: WT (D-WT) and ApoE [D-ApoE(-/-)]. The C group received no treatment for 8 weeks. In the D group, the maxillary molar cusps were cut off for 8 weeks. The spatial memory of rats was assessed according to their behavioral performance in a radial arm maze. In both genotypes of rats, significant differences in the reference memory, Aβ42 production, β-secretase expression and plasma corticosterone levels were observed between the C and D groups (P < 0.0125). The levels of Aβ42 and glucocorticoid receptor in the C-ApoE(-/-) group were also significantly higher than those in the C-WT group (P < 0.0125). However, no significant differences in these parameters were found between the two genotypes with occlusal disharmony. In conclusion, occlusal disharmony induces cognitive dysfunction and Aβ accumulation in the rat hippocampus, and the effects of occlusal disharmony on Aβ accumulation and cognitive dysfunction were larger than those of apoE deficiency.