Bystander mechanisms that originate in the areas surrounding a tissue damage presumably play an important role participating in wound healing and tissue remodeling. Thus identification and characterization of bystander mechanisms will help to development of new treatments of patients with a radiation exposure. In the present study we irradiated 3-dimensional tissue model of human epidermis Epi-200 (Mat-Tek Ashland MA) with 2.5 Gy protons. By exposing only a thin strip across the center of the EPI-200 tissue we have been able to measure global gene expression responses in directly irradiated and bystander cells located at 0.125-0.375 0.375-0.625 0.625-875 mm from the irradiation line. The data were analyzed using BRB-Array Tools (NIH) and further gene ontology analysis and network analysis was performed with Panther (Applied Biosystems) and IPA (Ingenuity) accordingly. Significantly responding genes were identified at all distances and included sets common to both direct and bystander responses. False discovery rate in bystander samples did not exceed 20% (p=0.001) and was sufficiently low in the samples obtained after the whole tissue exposure (0.06-1.16%). Analysis of the fragments cut at the same distance revealed 52 54 and 88 differentially expressed genes. These gene lists overlapped each other had from 3 to 12 genes in common including CLED2 S100A7A. Samples obtained after the whole tissue exposure discovered 949 differentially expressed genes. Moreover the performed gene ontology analysis showed there overrepresentation of TP53 pathway (pathways p=2.04E-02) a common marker of direct irradiation response and also overrepresentation of the following groups of genes: signal transduction (p=4.52E-04) cell communication (p=1.24E-04) and cell cycle in the category of biological processes; DNA helicase activity (p=2.54E-07) receptor binding (p=6.19E-04) calcium ion binding proteins (p=2.57E-03) as the molecular functions. Differentially expresses genes of bystander samples had few categories in common such as cell communication (p=2.36E-03) and signal transduction (p=2.42E-03) among the biological processes and receptor activity (p=4.54E-03) among the molecular functions. Categories specific for the bystander samples included G-protein coupled receptors (p=7.24E-03) and ligand-gated ion channels (p=4.16E-03) suggesting a role of external stimulation and ion trafficking in bystander mechanisms. Radiation induced gene expression in 3-dimensional tissue model Epi-200 was measured in 16 hours after exposure to 2.5 Gy of protons. Four independent experiments were performed for the samples collected at different distances from the irradiation line (125-375 375-625 and 625-875 micrometers) using three tissue fragments per a data point. Moreover three sets of whole tissue irradited samples were also generated for 0 and 2.5 Gy (6 samples total) and used for comparison of bystander and direct responses.