Problem-based learning (PBL) is an instructional approach in which students in small groups engage in an authentic, ill-structured problem, and must (1) define, generate and pursue learning issues to understand the problem, (2) develop a possible solution, (3) provide evidence to support their solution, and (4) present their solution and the evidence that supports it (Barrows, How to design a problem-based curriculum for the preclinical years. Springer Publishing, New York, 1985). However, research has shown that novice problem-solvers and learners without deep content knowledge have difficulty developing strong evidence-based arguments (Krajcik et al., J Learn Sci 7:313-350, 1998a; Reiser, J Lear Sci 13(3):273-304, 2004). In this paper, we discuss the components of (e.g., claims and evidence) and processes of making (e.g., define problem and make claim) evidence-based arguments. Furthermore, we review various scaffolding models designed to help students perform various tasks associated with creating evidence-based arguments (e.g., link claims to evidence) and present guidelines for the development of computer-based scaffolds to help middle school students build evidence-based arguments.