In natural ecosystems, brown-rot fungi are major biodegrading agents acting on standing trees and dead wood. Decay caused by basidiomycetes results in structural instability and therefore negatively affects the quality and quantity of wood produced. Fungal attack can also trigger defense mechanisms within the tree aimed at delaying or halting the progress of infection. As the defense mechanisms active within the tree can decrease the value of its wood, their identification and study is of foremost importance. In this work, healthy trees of Eucalyptus grandis—a widely commercialized species in Uruguay—were inoculated with Laetiporus sulphureus and Gloeophyllum trabeum. The decay process was characterized in terms of chemical and anatomical changes, and the defense mechanisms elicited by the tree were identified. Although no visibly apparent symptoms of infection were detected 3 months after inoculation, microscopic analysis revealed anatomical and chemical changes (weakening, delamination and rupture of vascular and parenchymal cells) and decreased holocellulose and lignin contents. Compartmentalization and the production of kino were used by the tree as defense mechanisms.