Objective Previous studies suggested that overerpression of Slit2 results in abnormal Alzheimer’s disease-like behavior and cognition impairment in mice. The aim of this study is to investigate the relationship between overerpression of Slit2 and accumulation and clearance of amyloid-β in aging mice by comparing the differential expression of genes for accumulation and clearance of amyloid-β in aging Tg-Slit2 and Tg-2576 mice. Methods 14-month old male C57BL/6, Tg-Slit2 and Tg-2576 mice were used to detect the expression of Aβ1- 40 and Aβ1- 42 in brain by immunohistochemistry. Further, the total RNA in the brain of these mice were extracted, identified and inversely transcripted to cDNA, then the cDNA was detected by PCR array. The expression of genes in the brain of Tg-Slit2 and Tg- 2576 mice were analyzed. Results Comparing with the Tg-2576 mice in the same age, accumulation of Aβ was not found in the brain of Tg-Slit2 and C57BL/6 mice. The result from PCR array analysis showed that comparing with the same aged C57BL/6 mice, there were 16 up-regulated genes and 8 down-regulated genes in the brain of Tg-Slit2 mice and 14 up- regulated genes and 17 down-regulated genes in the brain of Tg-Slit2 mice. The expression of amyloid beta precursor protein (APP) in the brain of the three group mice was not changed. The expression of presenilin 2 (Psen2) related with Aβ production was significantly up-regulated in the Tg-2576 mice. In addition, the expression of low density lipoprotein receptor-related protein (LRP) 6 and 9 were markedly decreased in the Tg-2576 mice. Notably, these genes were not changed in the brain of the aging Tg-Slit2 mice. Conclusions The accumulation of Aβ in the brain are not found in 14-month Tg-Slit2 mice, In addition, different from Tg-2576 mice, the significant changes of expression of Aβ-related genes is not found in the brain of Tg-Slit2 mice.