Thiamine deficiency (TD) has known to induce cognitive dysfunction including deficits in memory formation known as Wernicke-Korsakoff's syndrome in human. However, mechanisms by which TD leads to deficits in learning and memory still remain unclear. In this study, to understand them, we examined effects of pyrithiamine-induced thiamine deficiency (PTD) on learning and memory in mice by performing behavioral and anatomical analyses. PTD-treated mice displayed body weight loss and motor ataxia just after the PTD treatment. However, PTD-treated mice showed comparable body weight and motor performance compared with control mice 3 weeks after PTD treatment, suggesting that PTD-treated mice displayed recovery from severe deficits in body weight and motor performance. In contrast, PTD-treated mice showed impairments in formations of social recognition, contextual fear, novel object recognition and spatial memories 3 weeks and 3 months after the PTD treatment, suggesting that the PTD-treatment led to chronic impairments in formations of hippocampus-dependent memories. On the other hand, PTD-treated mice showed normal formation of amygdala-dependent memory. Importantly, anatomical analyses indicated that PTD-treated mice displayed significant decrease in sizes of hippocampus. Our results indicated that PTD-treatment led to impairments of hippocampus-dependent memory and an atrophy of hippocampus area, suggesting that PTD-treatment impairs the function of hippocampus.