The symptoms of the clubroot disease on Brassica species caused by the obligate biotrophic protist Plasmodiophora brassicae relies, among other factors, on the modulation of plant hormones. Signaling, transport as well as biosynthesis and metabolism are key features how the levels of auxins and cytokinins are controlled. We here describe (a) how to inoculate the model plant Arabidopsis thaliana with P. brassicae, (b) qualitative and quantitative methods to evaluate disease severity in auxin and cytokinin mutants, (c) molecular methods to monitor changes in plant and pathogen transcripts, (d) prerequisites for the establishment of transgenic lines manipulated in an auxin or cytokinin pathway, and (e) methods for β-glucuronidase staining in root galls and sections of infected roots to determine auxin and cytokinin responsive promoter activities.