A method for the isolation of caftaric, coutaric and fertaric acids from grape pomace by high-speed counter-current chromatography (HSCCC) was developed. Using a system of hexane/ethyl acetate/methanol/water 3:7:3:7 (v/v/v/v) and 0.5% trifluoroacetic acid (TFA) in the head-to-tail elution mode, the target compounds were separated from co-extracted polyphenolics and subsequently isolated in a second run (tert-butyl-methyl ether/acetonitrile/n-butanol/water, 2:2:1:5 (v/v/v/v) and 0.5% TFA; tail-to-head elution mode). The concomitant flavonoid quercetin 3-glucuronide was also isolated with the present method. The compounds were characterized by 1H NMR spectroscopy, by LC/electrospray ionization (ESI)-MS/MS in the negative ionization mode, and by UV spectroscopy. A purity of 97.0% (2.0% Z-isomer) for caftaric acid, 97.2% (4.8% Z-isomer) for coutaric acid, and 90.4% (13% Z-isomer) for fertaric acid was obtained from 10 g of grape pomace with yields of 62, 48 and 23%, respectively. Caftaric and coutaric acids may be used for in vitro and in vivo studies and as reference substances for analytical purposes.