Several stages of the disease cycle of root rot of alfalfa caused by Phoma medicaginis var. medicaginis were studied by using scanning electron and light microscopy. First activity of the pathogen was the external colonization of the root. The pathogen penetrated directly causing discoloration and tissue disintegration. Inter- and intracellular penetration facilitated by enzymatic degradation was likely the mechanism involved in breaching the barrier of the epidermal cells. Colonization of the cortex was intercellular. Radial access to the xylem elements was achieved through the cortex. Host responses to invasion by the pathogen were suberization of cortical cell walls and occlusion of vessels with pectic substances and wound gum. Cavities in the cortex resulting from tissue degradation were associated with later stages of infection. Intracellular hyphae were observed in dead cells of the cortex and in the xylem.