Whereas an RBE > 1 is described for very low-energy X-ray beams (in the range of 25–50 kV), there is a consensus that the RBE of X-rays (from 0.1 to 3 MeV) is equal to 1, whatever the energy or dose rate of the beam. Comparisons of X-ray beam dose rates are scarce even though these beams are widely used in medical diagnosis or radiotherapy. By using two dose rates (0.63 and 2.5 Gy.min −1) of high-energy X-rays on normal endothelial cells (HUVECs), we have studied the clonogenic assay, but also viability/mortality, cell cycle analysis and measured cellular senescence by flow cytometry, and have performed gene analysis on custom arrays. In order to consolidate these data, we performed localized irradiation of exteriorized small intestine at 0.63 and 2.5 Gy.min −1. Interestingly, in vivo validation has shown a significantly higher loss of weight at the higher dose when irradiating to 19 Gy a small fragment of exteriorized small intestine of C57Bl6J mice. Nevertheless, no significant differences were observed in lesioned scores between the two dose rates, while bordering epithelium staining indicated twofold greater severe damage at 2.5 Gy.min −1 compared to 0.63 Gy.min −1 at one week post-irradiation. Taken together, these experiments systematically show that the relative biological effectiveness of photons is different from 1 when varying the dose rate of high-energy X-rays. Moreover, these results strongly suggest that, in support of clonogenic assay, multiparametric analysis should be considered to provide an accurate evaluation of the outcome of irradiated cells.