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The importance of inter-organizational system (IOS) has been increasingly recognized by organizations and it is becoming vital and a competitive necessity due to globalization and the growing importance of business alliances, because organizations are interdependent for survival. Based upon intensive review of IOS development literature, special factors are influential in developing inter-organizational information systems that are different from factors in developing intra-organizational information systems. In this paper, all factors comprehensively have been identified and analyzed by using a system approach. Obtained findings suggested that there are six groups of factors that significantly affect on IOS development. Then significance and priority of the each factor by Shannon entropy were determined. Result of this research exhibit that relationship type between organizations is most important factor in IOS developing while in past researches less attention has been to IOS stakeholders.