This article introduces AI2D-RST, a multimodal corpus of 1000 English-language diagrams that represent topics in primary school natural sciences, such as food webs, life cycles, moon phases and human physiology. The corpus is based on the Allen Institute for Artificial Intelligence Diagrams (AI2D) dataset, a collection of diagrams with crowdsourced descriptions, which was originally developed to support research on automatic diagram understanding and visual question answering. Building on the segmentation of diagram layouts in AI2D, the AI2D-RST corpus presents a new multi-layer annotation schema that provides a rich description of their multimodal structure. Annotated by trained experts, the layers describe (1) the grouping of diagram elements into perceptual units, (2) the connections set up by diagrammatic elements such as arrows and lines, and (3) the discourse relations between diagram elements, which are described using Rhetorical Structure Theory (RST). Each annotation layer in AI2D-RST is represented using a graph. The corpus is freely available for research and teaching.