The purpose of the current study is to explore the impact of associating animations with concrete models on eleventh-grade students' comprehension of different visual representations in organic chemistry. The study used a post-test control group quasi-experimental design. The experimental group (N = 28) used concrete models, submicroscopic animations of molecules and chemical reactions to study an organic chemistry unit in their textbook. On the other hand, the control group (N = 22) used concrete models only. To assess students' comprehension of different visual representations in organic chemistry, a test called the Organic Chemistry Visualisation Test (OCVT) was designed and administered at the end of the study. The results indicated that the experimental group significantly outperformed the control group. Students in the experimental group, with the help of animations, were able to view multiple representations simultaneously, rotate molecules and inspect them from different angles, and comprehend the characteristics of organic molecules such as connectivity, chirality, bond angle, stereochemistry and the spatial arrangement of atoms within molecules. It was observed that the students in the experimental group were excited to navigate between different types of representations of the same molecule and to check whether they predicted its configuration (e.g. three-dimensional, two-dimensional or Fischer Projection models) correctly. Also, students were able to view more complex molecules using animations rather than concrete models. Limitations of the study and implications for teaching, learning, and further research are discussed.