Objective To investigate the distribution of free zinc ions and zinc transporter-6 (ZnT6) in the APP/PS1 transgenic mouse cerebellum. Methods Immersion autometallography (AMG) and immunohistochemistry were used to analyze the distribution of free zinc ions, amyloid precursor protein (APP) and ZnT6 in the APP/PS1 transgenic mouse cerebellum, respectively. Immunofluorescence and confocal laser scanning microscopy were used to analyze the relation between ZnT6 and Aβ in senile plaques. Results Zinc ions, APP and ZnT6 were mainly located in the amyloid plaques, which were predominately located in the molecular layer. The Purkinje cell layer and granular layer only contained a few plaques. Confocal microscopic results revealed a colocalization of ZnT6 and Aβ in the senile plaques. Conclusions The abundant expression of ZnT6 and accumulation of zinc ions in the β-amyloid plaques of the APP/PS1 transgenic mouse cerebellum, suggesting that zinc ions might be involved in the formation of senile plaques, while ZnT6 might play an important role in the regulation of zinc accumulation during the pathological process of Alzheimer’s disease.