Nuclear magnetic resonance (NMR) studies of mycorrhizal symbioses have illuminated a number of functional aspects of these complex associations. Here we review studies of the two main types of mycorrhiza (ectomycorrhizas and arbuscular mycorrhizas) to which NMR has been applied. Although the physiological questions addressed in each case are frequently the same, these two mutualistic symbioses are sufficiently different to justify separate discussion. In conjunction with isotopic labelling NMR is able to examine the transfer of substrates between the symbionts both in vivo and in vitro, as well as the production of secondary metabolites in response to colonization. In addition, this methodology is capable of determining the locations of the biosynthesis and translocations of storage compounds, such as polyphosphates, lipids and carbohydrates, in mycorrhizal fungi both in the free-living and in the symbiotic stages of their life cycle. NMR has been useful in analysing metabolism, transport and energetics, and the results of such studies have practical and ecological significance. Models of transport and physiology to which NMR has contributed form the necessary foundation for functional genomic exploration.