Metallothionein-3(MT-3), also known as growth inhibitory factor (GIF), is predominantly expressed in central nervous system (CNS). It belongs to the family of metallothionein(MT) but has several unique properties that are not shared by other family members such as MT-1/MT-2. In the past few years, MT-3 had been postulated to be a multipurpose protein which could play important neuromodulatory and neuroprotective roles in CNS besides the common roles of MTs. However, the primary function of MT-3 and the mechanism underlying its multiple functions were not elucidated so far. In present study, human neuroblastoma cell line SH-SY5Y was employed to study the overall cellular protein changes induced by transient transfection of MT-3 gene, based on comparative proteome analysis. Averagely about 750 spots were visualized by Coomassie staining in one 2D gel, in which 17 proteins were shown to display significant and reproducible changes by semiquantitative analysis with ImageMaster 2D Elite software. Among them, 12 proteins were up-regulated while other 5 proteins were down-regulated. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, 10 proteins were further identified to be zinc finger protein, glutamate transporter, and enhancer protein, etc., which were involved in several important pathways regulating the functions of central nervous system. The results showed that MT-3 might exert its unique functions by regulating the expression of these proteins.