Chickpea is known as a plant that is rich in protein, carbohydrates, and nutrition, and its seeds and sprouts have been processed into various health foods. In the present study, four isoflavones were purified from the seeds and sprouts of chickpea by high speed countercurrent chromatography (HSCCC) using two biphasic solvent systems composed of n-hexane-ethyl acetate-methanol-water (5:5:5:5, v/v) and ethyl acetate-water (1:1 v/v). The results indicated that 14.2 mg of formononetin, 15.7 mg of biochanin A, 9.1 mg of ononin, 11.3 mg of biochanin A-7-O-β-D-glucoside were obtained from 150 mg of sprout extracts with the purity of 92.26%, 95.86%, 95.32%, and 96.56%, respectively. Compared with the sprouts, separation of seed extracts yielded less amounts of biochanin A-7-O-β-D-glucoside and biochanin A with lower purity. The results indicate that four main isoflavones in chickpea, i.e., isoflavones, formononetin, biochanin A, ononin, and biochanin A-7-O-β-D-glucoside, are substantially increased by biosynthesis during the seed germination.