The paper presents a framework for studying responses of mycorrhizal roots to external stresses, including possible feedback effects, which are likely to occur. A conceptual model is presented to discuss how carbon may be involved in singular and multiple stress interactions of mycorrhizal seedlings. Recent literature linking carbon allocation and host/fungal response under natural and anthropogenic stresses is reviewed. Due to its integral role in metabolic processes, characterizing carbon and carbon allocation in controlled laboratory environments could be useful for understanding host/fungal responses to a variety of natural and anthropogenic stresses. Carbon allocation at the whole plant level reflects an integrated response which links photosynthesis to growth and maintenance processes. A root-mycocosm system is described which permits spatial separation of a portion of extramatrical hyphae growing in association with seedling roots. The results are presented in a fashion to illustrate the nature of information which can be obtained using this system. Current projects using the mycocosms include characterizing the dynamics of carbon allocation under ozone stress, and following the fate of organic pollutants. The authors believe that the system could be used to differentiate fungal and host mediated responses to a large number of other stresses, and to study a variety of physiological processes in mycorrhizal plants.