The spatial organisation of soils is crucially important in affecting belowground function, and the associated delivery of ecosystem services. Fungi constitute an important part of the soil biomass. As well as playing key roles in nutrient cycling and biotic interactions, they are also intimately involved in soil structural dynamics. Fungi mediate the formation of soil structure at a variety of spatial scales via charge, adhesive and enmeshment mechanisms. They also produce large quantities of hydrophobic compounds that affect water infiltration properties of soils. Fungi can also destroy soil structure via decomposition of organic matter that affects soil aggregation. In turn, soil structure affects fungi. The filamentous growth-form of fungi is a very efficient spacefilling structure well adapted for life in a spatially heterogeneous environment such as soil, but the labyrinthine pore network ultimately regulates how fungal mycelia grow through and function within the soil. The distribution of water within soils plays a crucial role in governing fungal development and activity, as does the spatial distribution of nutrient resources. This article reviews the continual interplay that occurs between soil structure and fungi, and discusses how self-organisation mechanisms may operate in the soil system.