Scientific visualisations such as computer-based animations and simulations are increasingly a feature of high school Science instruction. Visualisations are adopted enthusiastically by teachers and embraced by students, and there is good evidence that they are popular and well received. There is limited evidence, however, of how effective they are in enabling students to learn key scientific concepts. This paper reports the results of a quantitative study conducted in Australian Chemistry classrooms. The visualisations chosen were from free online sources, intended to model the ways in which classroom teachers use visualisations, but were found to have serious flaws for conceptual learning. There were also challenges in the degree of interactivity available to students using the visualisations. Within these limitations, no significant difference was found for teaching with and without these visualisations. Further study using better-designed visualisations and with explicit attention to the pedagogy surrounding the visualisations will be required to gather high quality evidence of the effectiveness of visualisations for conceptual development.