Embryo assessment is currently performed through the analysis of morphology and cleavage rate. Recent studies have sought to identify a correlation between quali-quantitative profiles of small molecules of metabolic interest and the outcome of embryo transfer. Approaches relying on both optical and non-optical spectroscopy have been proposed to non-invasively monitor the embryo culture media. However, the non-invasive approach only offers an indirect strategy to monitor embryos and a turn-around solution to bypass the limits of detection of these analytical techniques. In this paper we pave the way for direct metabolic assessment of embryos through the mass-spectrometry-based analysis of blastocoele fluid, which is withdrawn from the blastocoele cavity prior to cryostorage of blastocysts. We conclude that it is possible to detect most of the metabolites of potential interest right at the very heart of the blastocyst, without disrupting the workflow of a classic laboratory pipeline.