Limonoids are tetranortriterpenoids of considerable interest due to their structural varieties and biological activities, such as insecticidal, antibacterial, antifungal, antimalarial, anticancer and antiviral. They contain oxygen atoms that confer a moderate polarity and are responsible for the difficulties in their separation by traditional chromatographic methods. High-speed countercurrent chromatography (HSCCC) is a versatile liquid-liquid separation technique, in which the sample is distributed between two non-miscible phases to achieve separation. To isolate limonoids from a complex Carapa guianensis seed extract by gradient elution HSCCC and to identify them by spectrometric and spectroscopic methods. The hexane extract of Carapa guianensis squeezed seeds was prepared by Soxhlet extraction. From this extract, 800 mg were submitted to gradient mode HSCCC, using the solvent systems hexane:ethyl acetate:methanol:water 1:2:X:1, X = 1.5 (system A) and X = 1.75 (system B). The upper organic phase of the system A was used as stationary phase, and the lower aqueous phases of both systems as mobile phases. In this procedure, 165 fractions of 4 mL (660 mL) were collected. Six compounds were isolated. Spectrometric and spectroscopic analysis allowed the identification of the substances, as follows: methyl angolensate (28.7 mg), 7-deacetoxy-7-oxogedunin (17.9 mg), deacetylgedunin (3.7 mg), 6alpha-acetoxygedunin (40.1 mg), gedunin (21.0 mg), and andirobin (5.8 mg). The use of gradient mode in HSCCC was a good alternative, exploiting small variations of partition coefficient between the substances. Thus it was possible to isolate them in a good relative abundance, compared with classical chromatographic methods.