This paper describes the isolation of flavonoids and other aromatic compounds from an ethyl acetate extract of leaves of Siparuna glycycarpa using stepwise elution counter-current chromatography (CCC). The elution profile yielded the following compounds: diglycosylated flavonoids, quercetin 3-O-rutinoside and quercetin 7-O-rutinoside, followed by monoglycosylated flavonoids, kaempferol-3-O-β-glucopyranoside, kaempferol-3-O-β-rhamnopiranoside, kaempferol-3-O-β-6''(p-coumaroyl) glucopyranoside, and quercetin-3-O-β-glucopyranoside, and then free phenolics, protocatechuic acid and 2',6'-dihydroxy-4, 4'-dimethoxydihydrochalcone, which shows that this type of elution covers a broader range of polarity than the traditional isocratic mode. This makes it more suitable to perform separations of mixtures containing large differences in hydrophobicity. A GC analysis of a blank CCC run was performed to determine if changes in the mobile phase composition affect the chromatographic process. Results showed a gradual variation of the composition of the mobile phase emerging after the step gradient, favoring the selectivity of the solvent system. This article is protected by copyright. All rights reserved.