This article reviews the current status of three-dimensional reconstruction as a tool in the understanding of microscopical morphology. Many microscopical structures have a three-dimensional shape that cannot readily be appreciated by the study of sections alone. Three-dimensional reconstructions often provide novel information about such structures and enable researchers to formulate new hypotheses about the subject of their study. This review concentrates primarily on the methodology involved and how it is used to generate three-dimensional images and to provide three-dimensional quantitative data.