In this study, we compared interactions of two Melampsora foliar rust species with poplar, which resulted in either limited or abundant pathogen proliferation. In the pathosystem exhibiting limited pathogen growth, a defence response was observed after invasion of poplar leaf tissues by the biotroph, with late and clear production of reactive oxygen species (ROS) and other products. Characterisation of the histological, biochemical and transcriptional events occurring in both pathosystems showed striking similarity with components of plant defence reactions observed during qualitative resistance. Key components associated with development of an active defence response, such as up-regulation of pathogenesis-related (PR) genes, were observed during infection. Moreover, the time course and strength of gene induction appear to be critical determinants for the outcome of the tree–pathogen interaction. This work provides basic biochemical characterisation and expression data for the study of so-called partial resistance in the poplar–rust pathosystem, which is also applicable to other plant–pathogen interactions resulting in quantitative disease resistance.