In a series of three experimental studies, the effectiveness of three-dimensional computer simulations to aid the understanding of chemical structures and their properties was investigated. Arguments for the usefulness of three-dimensional simulations were derived from Mayer's generative theory of multimedia learning. Simulations might lead to a decrease in cognitive load and thus support active learning. In our studies, the learning effectiveness of three-dimensional simulations was compared to two-dimensional illustrations by use of different versions of a computer programme concerning the modifications of carbon. The first and third study with freshman students of chemistry and biochemistry show that no more knowledge was acquired when participants learnt with three-dimensional simulations than with two-dimensional figures. In the second study with 16-year old secondary school students, use of simulations facilitated the acquisition of conceptual knowledge. It was concluded that three-dimensional simulations are more effective for younger students who lack the experience of learning with different visual representation formats in chemistry. In all three studies, a significant relationship between spatial ability and conceptual knowledge about the modifications of carbon was detected.