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The purification of emodin in an aqueous two-phase system (ATPS) composed of tert-Butanal and sodium chloride was optimized by using response surface methodology (RSM). A central composite design was used to evaluate the influence of initial emodin concentration, pH, and concentration of tertButanol and sodium chloride on the extraction yield of emodin. The optimum conditions were determined as emodin 6.49μg/ml, pH 4.27, tert-Butanol 0.25 % (v/v) and sodium chloride 0.11g/ml. It was observed that sodium chloride increased emodin partitioning. The optimal condition gave a yield of 92.04% for emodin partitioning and it was a good result for a first step purification.