Bud dormancy in temperate woody perennials is a complex process consisting of three different stages; paradormancy, endodormancy, and ecodormancy. Endodormant buds differ from the other types of dormant buds in that they cannot resume growth under favorable conditions. Because endodormant buds require a certain amount of chilling accumulation for the transition to ecodormancy, genes showing chilling-mediated differential expression patterns are candidates for internal factors controlling endodormancy. To search for genes controlling the endodormancy of Japanese apricot (Prunus mume Sieb. et Zucc.), we performed 454-pyrosequencing to examine gene expression patterns of the dormant leaf and flower buds of Japanese apricot at three different stages of dormancy. We also used buds from branches that had been collected at the endodormant stage and treated with cold or non-cold temperatures. From 485,376 reads generated, we obtained 28,382 contigs and 85,247 singletons, of which 47,401 (41.7%) were annotated by BLAST searches against the non-redundant NCBI protein/nucleotide database. Among them, only 2,530 sequences showed high sequence similarity to Prunus genes in the database, while the remaining 44,871 sequences showed similarity to known genes of other genera and were novel in Prunus. Functional classification by the gene ontology (GO) term indicated that the genes obtained in this study function in a relatively wide range of biological processes. We searched for up-regulated genes in endodormant leaf and flower buds and found that 74 and 82 genes, respectively, were up-regulated at the endodormant stage as compared with the paradormant stage. About one-third of them, 21 and 25 genes in the leaf and flower buds, respectively, were down-regulated at the ecodormant stage as compared with the endodormant stage. P. mume DORMANCY-ASSOCIATED MADS (PmDAM) genes were among those that were up-regulated preferentially in endodormant buds. From the EST data obtained, we constructed a “Japanese apricot dormant bud EST database” (JADB) for future studies on dormancy in Prunus.