The research which led to this Ph.D. dissertation was carried out under the guidance of Prof. Jayashree Ramadas at the Homi Bhabha Centre for Science Education, Tata Institute of Fundamental Research, Mumbai. We investigated how middle school students use visual and verbal forms of thinking, reasoning and communication to express understanding of the human body. Understanding of structure, function and the relationships between them in the context of the digestive, the respiratory and the circulatory systems was probed. We assessed their basic knowledge using a scheme, based on a common conceptual framework encompassing structure and function, which was used to code both text and diagrams. Transformational reasoning and analogical thinking were used as research tools in the form of tasks to probe visualisation of body systems. Overall, the results showed that students were more comfortable expressing their understanding through text rather than through diagrams. Structure concepts were understood better than function. Common alternative conceptions relating to the body systems were identified. The results have led us to draw some implications for pedagogical practices in Biology.