The clubroot disease of cruciferous crops is caused by an obligate biotrophic protist, Plasmodiophora brassicae. The disease is characterized by the development of large root galls accompanied by changes in source-sink relations and the hormonal balance within the plant. Since the disease is difficult to control, it is of high economic interest to understand the events leading to gall formation. In this review we will give an overview on the current knowledge of changes brought about in the host root by this obligate biotrophic pathogen. Emphasis will be on the regulation of changes in plant hormone homeostasis, mainly auxins and cytokinins; the possible role of secondary metabolites, especially indole glucosinolates, in gall formation and auxin homeostasis will be discussed. Also, results from mutant analysis and microarrays using the model plant Arabidopsis thaliana are presented.