The structures of metabolites produced in microgram quantities by enzymatic reductions with baker's yeast were analyzed using the crystalline sponge method. The X-ray data provided reliable structures for trace metabolites including their relative and absolute stereochemistries that are not fully addressed by conventional NMR and LC-MS analyses. Technically, combining two or more chromatographic purification techniques is essential because, unlike abundant synthetic compounds, extracted metabolites contain many low level UV-silent impurities. The crystalline sponge method coupled with HPLC purification (LC-SCD) would thus be a useful method for metabolic analysis and drug discovery.