The mechanisms of BTH [benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester]-induced resistance against bean rust caused by Uromyces appendiculatus have been explored in Phaseolus vulgaris by light and transmission electron microscopy, following the infection progression in plants challenged 7 days after treatment. While BTH did not affect uredospore germination and fungal penetration in the substomatal cavity, a first impairment to the colonization appeared evident about 48-96 h after inoculation, with alterations of infection hypha structure and reduction in mycelium expansion. No differences were found in this phase regarding the formation and ultrastructure of haustoria in untreated and BTH-treated plants, except for the deposition of electron-opaque material in the extrahaustorial matrix of the latter. A second and decisive impairment in fungal progression was observed at 7-10 days after inoculation when host cell penetrated, or in close contact with the fungal hyphae, were impregnated by phenolic compounds. The same was observed in fungal walls, particularly around haustoria, thus hampering the biotrophic habitus of the fungus and further mycelium spreading. This, in turn, prevented the evasion of fungal reproductive structures, the uredinia, and the appearance of visible symptoms. No particular ultrastructural alterations were observed in most of the penetrated cells, even at late stages of infection, indicating that BTH treatment does not induce host cells to respond with a hypersensitive reaction (HR). A parallel time course of the expression of phenylalanine ammonia lyase (PAL) gene, the key enzyme for the synthesis of phenylpropanoidic phytoalexins and many other phenolics, has shown that PAL mRNA is strongly and persistently transcripted in BTH-treated plants since the 6th h after treatment, though no apparent ultrastructural alterations were detectable up to some days after pathogen challenging. This indicates that BTH, at the employed concentration of 0.3 mM, directly activates the plant's own defences, thus accounting for the observed full protection against bean rust.