Students engaged in problem-based learning (PBL) units solve ill-structured problems in small groups, and then present arguments in support of their solution. However, middle school students often struggle developing evidence-based arguments (Krajcik et al., "J Learn Sci" 7:313-350, 1998). Using a mixed method design, the researchers examined the use of computer-based argumentation scaffolds, called the "Connection Log," to help middle school students build evidence-based arguments. Specifically we investigated (a) the impact of computer-based argumentation scaffolds on middle school students' construction of evidence-based arguments during a PBL unit, and (b) scaffold use among members of two small groups purposefully chosen for case studies. Data sources included a test of argument evaluation ability, persuasive presentation rating scores, informal observations, videotaped class sessions, and retrospective interviews. Findings included a significant simple main effect on argument evaluation ability among lower-achieving students, and use of the scaffolds by the small groups to communicate and keep organized.