This chapter investigates the pedagogical issues of student electronic portfolios (e-portfolios) in the context of personalized instruction for undergraduate education. The discussion elaborates on the educational potential of an e-portfolio system in facilitating an outcomes-based assessment of student achievements. The chapter illustrates practical examples of integrating theory and practice aimed at assisting a meaningful investigation of an e-portfolio system with a focus on inquiry-based student assessment. The objective of such an inquiry is to enhance and encourage student learning, especially learning by doing. Key issues and the necessary institutional support for an outcomes-based and personalized model of education in support of a portfolio learning system are identified. The interrelationship of portfolio assessment to curriculum and pedagogy and required changes to teaching and learning are described. The relevant learning theories that underpin the portfolio form of assessment are deliberated to caution how best to manage the use of e-portfolios for student learning and assessment. Looking beyond, it is expected that the e-portfolio system is an important element to support outcomes-based education involving collaboration from both faculty and students in pursuit of a quality learning experience. © 2010, IGI Global.