This study investigated similarities and differences between students’ experience in the research-based and traditional laboratory. The goal was to determine if the students’ laboratory experience influenced their understanding of the nature of experiments and experimental design. The data suggest that the students’ experiences differed between the laboratories, which resulted in students reporting different learning gains. The data support the idea that the research-based laboratory is more cognitively challenging compared to the traditional laboratory. The research-based laboratory required the students to develop hypotheses and investigations to explore their hypotheses. This process is missing from the traditional laboratory. In addition to being a cognitively challenging experience, the research-based laboratory also affords students the opportunity to use creativity which helped to enhance students’ understanding of the use of creativity by scientists. Neither laboratory was superior to the other for the facilitation of students’ understanding of hypotheses. In addition, students in both groups showed similar experimental design abilities.