Extracts from saffron, the dried stigmata from Crocus sativus L. are recognized as valuable tools for pharmaceutical development in neuroprotection and antidepressive therapy. One major lead compound is crocin-1 (1), which gets metabolized to the C20-dicarboxylic acid trans-crocetin (2) being responsible for potential NMDA-antagonistic effects in the central nervous system. Neither crocin-1 nor crocetin are commercially available in sufficient quality and to a reasonable price. The following protocol describes effective methods to obtain both compounds from an EtOH–water extract (2:8) in good yields (about 43% related to the starting material). Crocin-1 (purity>90%) can be obtained from the extract by means of partition chromatography (FCPC) in a single run without fractionation of the mobile phase by using only the stationary phase and in yields of about 48%, related to the saffron extract. Trans-crocetin can be obtained from the EtOH–water extract by enzymatic deglycosylation of crocins using commercially available cheap glycosidase mixtures as e.g. Röhm Enzyme® or RohamentCL®. Further polishing can be achieved by flash chromatography on MCI® stationary phase with yields between 6 and 11%.The protocols described provide effective isolation of crocin-1 and trans-crocetin reference compounds for further preclinical and analytical studies with saffron extracts.