In building cooperative distributed information systems, a methodology for analysis, design and implementation of security requirements of involved data and processes is essential for obtaining mutual trust between cooperating organizations. Moreover, when the information system is built as a cooperative set of e-services, security is related to the type of data, to the sensitivity context of the cooperative processes and to the security characteristics of the communication paradigms. This paper presents a methodology to build a trusted cooperative environment, where data sensitivity parameters and security requirements of processes are taken into account. The phases are illustrated and a reference example is presented in a cooperative information system and e-applications. An architecture for trusted exchange of data in cooperative information system is proposed. The requirements analysis phase is presented in detail.