Mycorrhizal researchers are faced with the dilemma of designing experiments on small-scale processes that contribute to the solution of large-scale problems, such as global change. Hierarchy Theory provides a paradigm that indicates the need for mycorrhizal research and suggests criteria that help to prioritize research objectives. In general, mycorrhizal research is justified whenever direct or indirect effects on mycorrhizal physiology or ecology form a critical constraint to large-scale system function. The paper attempts to extract the relevant concepts from the theory and provides a series of illustrative examples from mycorrhizal research.