The infection process of Alternaria cirsinoxia was studied on Canada thistle (Cirsium arvense) in the controlled environment and in the field. In the controlled environment, germination of conidia began at 2 h and appressoria formation at 4 h after inoculation. Approximately 75% of appressoria formed at the anticlinal wall junctions of the epidermis. Leaf penetration occurred between 6 and 24 h, most commonly in between adjoining anticlinal walls. Penetration through stomata was rare. After penetration, large, intracellular infection hyphae formed and branched within epidermal cells, ramifying throughout the leaf tissues inter- and intracellularly by 24 h. In field conditions, infection coincided with prolonged rainfall and conidia remained viable on the leaf surface for 8–9 days (d) before causing infection on leaves. A host response occurred after penetration, involving deposition of lignin and callose in the infected epidermal and mesophyll cell walls. High levels of silicon were detected in epidermal cells directly below appressoria, often appearing to form entirely silicified infected cells which were resistant to collapse after air-drying. This study shows that A. cirsinoxia has the potential for rapid invasion of the leaf tissues of Canada thistle under good moisture conditions. The implications of the host responses, in terms of defence against infection, are discussed.