An experiment was performed to observe protein changes in the hippocampus of zinc-deficient (ZD) rats. Twenty-four male weanling Wistar rats were randomly assigned to ZD (n = 12) and control groups (n = 12). After 4-wk treatment, we used 2-DE and MALDI-TOF-MS to analyze the proteomes of hippocampus in the two groups. One of the important differential proteins, ubiquitin C-terminal hydrolase L1 (Uch-L1), was confirmed by Western blot assays. The results demonstrated that compared with the controls, ZD rats had significantly reduced plasma zinc concentration and alkaline phosphatase activity. The latency period in passive avoidance performance was also significantly shorter for the ZD rats. Nine proteins were differentially expressed between the two groups. Eight of them were identified. Tubulin beta chain and voltage-dependent anion channel 1 were upregulated, while mitochondrial aldehyde dehydrogenase, a-enolase, dimethylarginine dimethylaminohydrolase 1, F-actin capping protein alpha-2 subunit, pyruvate dehydrogenase beta and Uch-L1 were downregulated, respectively. Importantly, some of the identified proteins (e.g. Uch-L1) are known to be involved in cognitive impairment. Western blot analysis of hippocampus Uch-L1 expression confirmed the proteomic findings. The data indicated that there may be common mechanisms or pathways in cognitive dysfunction between neurodegenerative diseases and zinc deficiency.