The present volume contains the proceedings of the Third IPM International Conference on Fundamentals of Software Engineering (FSEN), Kish, Iran, April 15-17, 2009. FSEN 2009 was organized by the School of Computer Science at the Institute for Studies in Fundamental Sciences (IPM) in Iran, in cooperation with the ACM SIGSOFT and IFIP WG 2.2. This conference brought together around 100 researchers and practitioners working on di?erent aspects of formal methods in software engineering from 15 di?erentcountries.ThetopicsofinterestinFSENspanoverallaspects offormal methods,especiallythoserelatedtoadvancingtheapplicationofformalmethods in software industry and promoting their integration with practical engineering techniques. The Program Committee of FSEN 2009 consisted of top researchers from 24 di?erent academic institutes in 11 countries. We received a total of 88 submissions from 25 countries out of which the Program Committee selected 22 as regular papers, 5 as short papers, and 7 as poster presentations in the conferenceprogram.Eachsubmissionwasreviewedbyatleastthreeindependent referees, for its quality, originality, contribution, clarity of presentation, and its relevance to the conference topics. This volume contains the revised versions of the regular and short papers presented at FSEN 2009. Three distinguished keynote speakers delivered their lectures at FSEN 2009 on models of computation: automata and processes (Jos Baeten), veri?cation, performanceanalysisandcontrollersynthesisforreal-timesystems(KimLarsen), and theory and tool for component-based model-driven development in rCOS (Zhiming Liu). Our invited speakers also contributed to this volume by s- mitting their keynote papers, which were accepted after they were reviewed by independent referees.