In the present study, we examined whether the ARNTL (BMAL1) rs2278749 T/C polymorphism was associated with the susceptibility to Alzheimer disease (AD). This case-control study examined the genotypes of apolipoprotein E (APOE e4) and BMAL1 rs2278749 T/C using restriction fragment length polymorphism and the TaqMan assay, respectively. A total of 296 unrelated AD patients and 423 control subjects were included. Both in the entire sample and in APOE e4 non-carriers, the prevalence of T carriers in BMAL1 rs2278749 T/C in AD patients was significantly higher than that in control subjects (entire sample: χ(2) = 12.950, P < 0.0001; APOE e4 non-carriers: χ(2) = 13.094, P < 0.0001). Both in the entire sample and in APOE e4 non-carriers, the prevalence of TT genotypes 2278749 in AD patients was also significantly higher than that in control subjects (entire sample: χ(2) = 7.765, P = 0.024; APOE e4 non-carriers: χ(2) = 13.062, P < 0.0001). However, among APOE e4 carriers, the difference in the prevalence of T carriers or TT genotypes in the BMAL1 rs2278749 T/C between patients and control subjects presents was not significant (T carriers: χ(2) = 0.078, P = 0.851 or TT genotypes: χ(2) = 2.576, P = 0.325). Among APOE e4 non-carriers, T carriers in the BMAL1 rs2278749 T/C were associated with a high susceptibility to AD, but among APOE e4 carriers, the association between AD and BMAL1 rs2278749 T/C was not significant.