Seed dormancy is regulated by complex networks in order to optimize the timing of germination. However, the biochemical basis of the regulation of seed dormancy is still poorly understood. Many temperate timber species, which are of ecological and/or economic interest, are deeply dormant in seeds, such as Prunus campanulata. Freshly harvested seeds require warm plus cold stratification to break dormancy before they can begin to germinate. According to the results of germination, both warm and cold stratifications are the critical influences for breaking seed dormancy. Significant variations in seed proteins were observed by 2-DE before and after the breaking of seed dormancy. Among the 320, 455, and 491 reproducibly detected spots on the cotyledons, embryos, and testae, respectively, 71 dramatic changes in abundances were observed following warm and/or cold stratification. Among these protein spots, dehydrin, prunin 1 precursor, prunin 2 precursor, and prunin 2 were identified by MS and sequence comparison. The implications of protein changes in relation to the breaking of seed dormancy and germination are discussed. This is the first report of a proteomic analysis of dormancy breaking in woody plant seeds.