This research aimed to develop and evaluate a visualization approach for teaching Organic Chemistry at Senior Cycle in Ireland. The Organic Chemistry through Visualisation (OCV) programme was designed to promote students’ (i) understanding of the inter-relation between different representations of organic molecules and (ii) their ability to predict the physical properties and reactivity of organic molecules. The use of physical models to promote accurate mental models of organic structures and development of student argumentation are core elements of the approach. Organic chemistry forms the basis of pharmaceutical chemistry, green chemistry, biochemistry and nanotechnology. However, in second-level teaching, this area of chemistry is often reduced to simply the rote learning of functional groups and their reactivity without development of understanding of the nature of this reactivity. Many organic molecules that students use in their everyday life are considered too complex in structure for second level students, for example vanillin. The approach adopted in this research ‘reduces’ complex molecules to ‘simply’ looking at each bond and asking where the electrons are located and how the molecule is constructed. By locating areas of high and low electron density in a molecule, it is possible to suggest reactive centres in the molecule and hence predict its reactivity. The findings of this research study indicate that while the majority of students were successful in translating between different representations, some still held 2-dimensional mental models of organic structures. The OCV approach was particularly successful in enabling students to predict and critically compare the physical properties of a range of organic molecules. Students were not only able to identify multiple reactive centres within organic molecules but also able to suggest the most likely reactive centre in the presence of electrophiles and nucleophiles. Following a full evaluation of the OCV approach, a suggested sequence for learning organic chemistry through the use of physical models has emerged. The results of this research have implications for the ongoing review of the current Leaving Certificate chemistry syllabus in Ireland.