Clubroot disease is a serious soil-borne disease caused by the obligate biotrophic Plasmodiophora brassicae in roots of cruciferous crops belonging to the Brassicaceae family. Glucosinolates (GSLs) are defense-related secondary plant products found in cruciferous plants that have been associated with clubroot disease. We investigated changes in total and individual GSLs in roots of rutabaga (Brassica napus subsp. rapifera Metzg) resistant ('Wilhelmsburger') and susceptible ('Laurentian') cultivars at an early stage of clubroot infection [7 days after inoculation (dai) with P. brassicae]. GSLs belonging to three major GSL groups, the aliphatic, aromatic, and indolic, were found in roots of both cultivars, with progoitrin being the most abundant GSL in both cultivars. Distinct patterns of various GSLs were observed in the roots of resistant compared to the susceptible cultivar. In general, the roots of the resistant cultivar had higher levels of aliphatic and aromatic GSLs than that observed in the susceptible cultivar. Indolis GSLs also can be precursors for the auxin indole-3-acetic acid (IAA), an auxin implicated in clubroot gall development. Roots of the clubroot-inoculated resistant cultivar showed a 17 % reduction in free IAA levels along with a 1.9-fold increase in the transcript abundance of BnIAGLU (codes for an enzyme that converts free IAA auxin to an inactive glucose eater conjugate) compared to its non-inoculated control at 7dai, suggesting that increased conjugation of free IAA to an inactive IAA-glucose ester could be associated with P. brassicae resistance. Overall, our current analysis suggests that GSLs play a role in inducing enhanced plant defense against the clubroot pathogen.