ABSTRACT: We have recently investigated the response of irradiated and bystander fibroblasts to heavy ions in confluent cultures exposed randomly to broadbeam and selectively to precision microbeam that target a predefined fraction of cells with counted number of particle(s), respectively, and found the difference in the time course of apoptosis induction and p53 phosphorylation between irradiated and bystander cells [Hamada MR2008]. In the present investigation, to further scrutinize the underpinnings of their temporally distinct responses, we set out to examine the gene expression changes in irradiated and bystander fibroblasts at a genome-wide level with the microarray analysis under the same experimental condition. We demonstrate that the gene expression profiles of bystander cells are substantially different from those of heavy ion-irradiated cells. Keywords: bystander effect, hour-time course cell number dependency, irradiation-dose response 36 samples ; Broadbeam control A, Broadbeam control B, Broadbeam sham 2 h A, Broadbeam sham 2 h B, Broadbeam sham 6 h A, Broadbeam sham 6 h B, Broadbeam D 2 h A, Broadbeam D 2 h B, Broadbeam D 6 h A, Broadbeam D 6 h B, Broadbeam 0.1D 2 h A, Broadbeam 0.1D 2 h B, Broadbeam 0.1D 6 h A, Broadbeam 0.1D 6 h B, Broadbeam 0.01D 2 h A, Broadbeam 0.01D 2 h B, Broadbeam 0.01D 6 h A, Broadbeam 0.01D 6 h B, Microbeam Control A, Microbeam Control B, Microbeam sham 2 h A, Microbeam sham 2 h B, Microbeam sham 6 h A, Microbeam sham 6 h B, Microbeam 1c 2 h A, Microbeam 1c 2 h B, Microbeam 1c 6 h A, Microbeam 1c 6 h B, Microbeam 5c 2 h A, Microbeam 5c 2 h B, Microbeam 5c 6 h A, Microbeam 5c 6 h B, Microbeam 25c 2 h A, Microbeam 25c 2 h B, Microbeam 25c 6 h A, Microbeam 25c 6 h B.