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Physiology is difficult for students to master because of the multi-level complex interrelationships among the systems and components. Systems modeling is a cognitive scaffolding tool that helps an individual conceptualize the underlying mechanism of a system by analyzing the inter-cause-effect relationships among the system components. To promote understanding of physiological concepts, systems modeling could facilitate students to articulate the complexity arising from simultaneous consideration of macro, micro, and systems level concepts and interactions. In this study, the undergraduate physiology students used systems modeling to construct models to represent the systems under study. The results showed the systems modeling group outperformed, though not significantly, the control group in both the immune and acid-base unit exam and final exam.