Abstract Study question Is micro-magnetic resonance (micro-MRS) a safe tool to non-invasively unravel the metabolic fingerprint of single mammalian embryos? Summary answer We successfully tested the safety of micro-MRS in a mouse model. No long or short-term adverse effect was found in vitro and in vivo. What is known already Non-invasive selection of the best embryo to transfer is one of the most significant challenges for ART professionals. The chemical sensitivity, resolving power, and, more importantly, the non-invasive nature of MRS makes it an excellent candidate to investigate the building blocks of complex organisms. Although MRS is a well-established technique for the biochemical profiling of large organisms, handling small samples like embryos and 3D cell cultures and spheroids alongside sensitivity issues has prevented its adoption for clinical and research applications. Our group has overcome these limitations with microchip-based sensors to leverage non-invasive MRS technology down to the embryo scale. Study design, size, duration This safety study was divided into two main phases in order to test all the components needed to operate the micro-MRS analysis. In phase 1 we used > 800 2-cell embryos to test a) radiofrequency exposure, b) device activation, and c) static magnetic field exposure. In phase 2 we confirmed in-vivo that MF exposure was not affecting live animals (n267) over 3 generations of mice by assessing different IVF outcomes, natural mating, live parameters and histopathology. Participants/materials, setting, methods Cryopreserved 2-cell B6D2F1 mouse embryos were purchased cryopreserved from JanvierLabs. In phase1 embryos were thawed and used for testing micro-MRS main components' safety. Mouse embryo assay (MEA) was used to first assess micro-MRS adverse effects in-vitro. In phase 2 embryos were exposed to magnetic field in a 9.4T Magnet for 1h at 37 °C, then surgically transferred to surrogate mothers. Both mothers and progeny were tracked up to F3. Statistical significance was set at p < 0.05. Main results and the role of chance This is the first study ever conducted to assess the safety and efficacy of micro-MRS on pre-implantation mammalian embryos. Our results show, with statistical significance, that micro-MRS is safe for use in mammalians. In particular, we have de-risked the three main aspects/components that could affect the embryos: 1) Materials to which the embryos are exposed when loaded into the device, 2) Radiofrequency energy required to activate the device and perform a measurement, and 3) Magnetic field required to analyze the embryos biochemistry in a non-invasive way. Overall no adverse effect was observed when the primary IVF outcomes were assessed, such as implantation rate and live birth rate. In addition, no visible alteration of the overall appearance of ED14.5 foetuses, F1, F2 and F3 mice was observed when comparing the mice obtained from treated or control embryos. The surrogate mothers did not display any significant alteration or visible health issues after embryo transfer. F1 and F2 mice were able to naturally mate and conceive new progeny suggesting that the reproductive potential of the animals is not affected by the magnetic field exposure. Furthermore, histopathological analysis of 5 representative organs did not reveal adverse effects on both surrogate mothers or F1 pups. Limitations, reasons for caution A vital step towards establishing MRS as a clinical and research tool is the reliable detection of a wide range of signals from cellular components. Our method is ready for R&D studies, while its clinical application requires further safety studies and protocol optimization. Wider implications of the findings A non-invasive quick assay would provide the means to reveal the role of embryonic lipids throughout development. Micro-MRS can further develop into a safe embryo assay for selection before embryo transfer. This would apply to both human and animal ART, whose success rate is relatively low. Trial registration number NA