The ectomycorrhizal symbiosis involving trees and soil fungi is a process of major ecological importance in forest ecosystems. The establishment of an effective symbiosis encompasses a series of complex and overlapping developmental processes in the colonizing mycelium and roots of host trees. Regulated gene expression is an important mechanism for controlling ectomycorrhizal symbiosis development and functioning. Gene profiling studies led to the identification of genes that are required for fungal attachment, plant defense, and symbiosis-related metabolism. They showed that changes in morphology associated with mycorrhizal development were accompanied by changes in transcript patterns, but no ectomycorrhiza-specific genes were detected. Comparison of the genomes of pathogenic and saprobic fungi with the recently released ectomycorrhizal Laccaria genome is providing crucial insights into the genetic makeup of plant–fungus interactions.