The clubroot disease is caused by the obligate biotrophic protist Plasmodiophora brassicae and is one of the most damaging for the family of Brassicaceae. Since many economically important crops belong to this plant family, the understanding of mechanisms how the disease is developing, are of high importance. Glucosinolates, a group of secondary plant products in the family of Brassicaceae, have long been associated with clubroot disease symptoms. Measurements showed that several glucosinolates are induced in root galls. While aliphatic glucosinolates are regarded as defense compounds, analysis of Brassica cultivars as well as Arabidopsis thaliana mutants provided correlative evidence between disease severity and indole glucosinolate content. The latter have been discussed as precursors for auxin biosynthesis. Since high auxin levels are associated with large root galls, indole glucosinolates could contribute directly or indirectly to the extent of disease development. Transcriptome and proteome experiments have revealed evidence for the involvement of genes from the glucosinolate and auxin pathway in gall formation. These data have been complemented by expression and mutant analysis. It can be concluded that regulation of glucosinolate and IAA biosynthesis might differ in Brassica and Arabidopsis.