The clubroot disease caused by the obligate biotrophic protist Plasmodiophora brassicae on host plants of the Brassicaceae family is characterized by enhanced cell division and cell expansion. Since a typical root section of an infected plant always includes different stages of the pathogen as well as uninfected cells, we were interested in investigating specific developmental stages of the pathogen and their effect on host transcriptional changes. We extended previous microarray studies on whole roots by using laser microdissection and pressure catapulting (LMPC) to isolate individual cells harboring defined developmental stages of the pathogen. In addition, we compared the central cylinder of infected plants with that of control plants. We were especially interested in elucidating the stage-specific hormonal network. The up-regulation of genes involved in auxin and cytokinin metabolism and signaling was confirmed. In addition, we found evidence that brassinosteroid (BR) synthesis and signal perception genes were in many cases up-regulated in enlarged cells and the central cylinder. This was confirmed by quantitative PCR. Treatment of wild-type plants with the BR biosynthesis inhibitor propiconazole reduced gall formation, and the analysis of the BR receptor mutant bri1-6 revealed less severe gall formation than in the respective wild type. Our results identify novel hormone pathways involved in clubroot development. Using LMPC to generate pools of homogeneous cell type populations combined with transcriptome analysis has been very useful to elucidate the regulation of gall growth by this obligate biotropic pathogen in a cell- and stage-specific manner.