Abstract: Objective To explore the molecular mechanism of bone marrow injury of acute irradiation syndrome, gene expression of bone marrow in mice after whole body irradiation was studied. Methods The molecular biology technology including suppression subtractive hybridization, cDNA array hybridization and Northern hybridization were used to study differential gene expression of mRNA level in bone marrow of C57BL/6J mouse 4h after 7Gy ⁶⁰Co γ-ray radiation in vivo. Results A series possibly induced genes after irradiation were obtained. The function of these genes related to cell cycle control, anti-oxidation, DNA repair, and hematopoiesis-immune response. The differential expression of CDKN1A and S100A8 gene were validated by further experiment. Conclusions The function of those differentially expressed genes after irradiation illuminated that radiation effects, such as DNA damage, cell cycle arrest and oxidation reaction which often happened in mammalian cells, also took place in bone marrow cells after irradiation. Furthermore, the hematopoiesis-immune function and the neuroimmunoendocrine regulation in bone marrow were also changed.