During meiosis, phosphorylation of H2AX is one of the earliest cellular responses to the generation of DNA double-strand breaks (DSBs) by the SPO11 topoisomerase. ATM is the kinase which mediates the formation of phosphorylated H2AX (H2AX) meiotic foci, while ATR is the kinase which signals chromosome asynapsis at the level of the XY bivalent. To investigate the possible role of ATR also in DNA damage signalling in meiotic cells, we studied the effect of UV radiation and chemotherapy drugs on H2AX phosphorylation and ATR relocalization in mouse pachytene spermatocytes. Here, we report that UV, a single strand break DNA-damaging agent, induces ATR relocalization from the XY sex body to nuclear foci and intense H2AX phosphorylation. Other DNA damage proteins such as MDC1, NBS1 and 53BP1 showed a similar relocalization following UVA microirradiation of spermatocytes. We found that DNA damage induced by UV increased the intensity and the number of H2AX foci also in Atm null spermatocytes. Inhibition of RNA synthesis was found to induce the formation of H2AX foci, but it did not influence the DNA damage response to UV irradiation. Finally, exposure of spermatocytes to double strand break DNA-damaging agents such as cisplatin, bleomycin or etoposide also induced ATR relocalization and intense H2AX phosphorylation and led to anomalies in synaptonemal assembly. Our results demonstrate that DNA damage induced by genotoxic stress can activate ATR and influence meiotic chromatin remodelling through H2AX phosphorylation, likely as part of a response which normally ensures germ cell genomic integrity.