This research is a prospective analysis of prioritizing research proposals using pre-established criteria and applying the Analytic Hierarchy Process-AHP. The prioritized projects should ensure the competitive advantage of the organization. For this analysis, criteria which take into account other factors, which are not purely technical, were applied. The guiding hypothesis of this study was that it is possible to maintain a competitive portfolio of research proposals, from the analysis of pre-established criteria, using the methodology of the Analytic Hierarchy Process, giving priority to innovation and technology transfer. A key finding was the importance of retrieving research projects’ history in the company, and stating gaps to be controlled in future analysis. Six ongoing projects were analyzed by 17 interviewed researchers and scores were given. Results obtained using the multicriteria analysis were similar to that previously applied by the selection committee, validating the hypothesis. We concluded that AHP may assist in the identification and prioritization criteria for project portfolio management.