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The Information Communication and Technology – ICT industry is facing a market of constant changes and challenges. These characteristics demand the ICT professionals to have a wide vision of the problem, rather than just knowledge on the technology. In this context, the objective of this article is to propose an innovative pedagogical methodology based on PBL (Problem Based Learning) to improve the learning effectiveness in software engineering, through the implementation of software factories, where students can work together to solve real problems. This methodology is running in a graduate course in Software Engineering managed by CESAR , a research institute with experience in the development of innovative software. Some important results about this course are presented and discussed in this paper.