Ionising radiation (IR) affects cellular and tissue function. However, the biological effects and interactions induced by IR are unclear. The aim of this study was to decipher the proteomic patterns that influence these pathways. The proteomes of Arabidopsis thaliana roots and rosettes were analysed in response to sub-lethal IR doses (0, 10, and 40 Gy). For each dose, the dynamic response was observed at different time points (2, 24 and 72 h). To quantitatively measure the effect of IR on the proteome, total proteins were extracted and subjected to 2-DE, and the changes in the 2-DE protein profiles were analysed. Statistical analysis revealed a total of 172 proteins (145 in leaves and 27 in roots) that were differentially expressed. These proteins were subsequently analysed by MALDI-TOF/TOF MS and comparative database analysis, and 144 (118 in leaves and 26 in roots) proteins were identified. The changes in the protein profile were quantitatively more significant for the 40 Gy dose than for the 10 Gy dose. In addition, specific functional groups of proteins were identified based on the consistency of the dose- and time-responses. The molecular mechanisms involved in the response to IR and a comparison of the observed responses are discussed.