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Previous studies on the performance evaluation of incubators have been based on more subjective oriented evaluation methodologies. This study utilized DEA(Data Envelope Analysis) methodology to evaluate 21 universitiesBIs in Seoul, Korea. As input factors, total operating expense, number of management manpower, total number of offices for incubation were selected. The number of graduating companies, the number of incumbents, and total amount of sales including exports were output variables for the proposed DEA model. Based on DEA model and analysis, comparative efficiency ratio and major inefficiency factors of each software incubator center were pinpointed. Possible ways to improve the efficiency of each incubator were suggested. This study contributes to the methodological ways of evaluating incubator management theoretically. Practically, DEA method will help incubator managers and government officials evaluate the efficiency of their management practices cooperatively.