Biofumigation, involving the growing of certain species of Brassicaceae and crushing and incorporating them into the soil at flowering, is attracting increasing interest for its potential use in Integrated Pest Management (IPM). One of the purposes of the program SYSBIOTEL, placed within the GIS PICleg (TM) framework, is to explore and disentangle the various effects of biofumigation on important epidemiological aspects concerning pathogen growth, inoculum production and activity, and the resulting disease of the host crop. After measuring the differences in the glucosinolate profiles of two Indian mustard (Brassica juncea) lines, an in vitro comparison was made of the effect of the volatile compounds released from their crushed aerial parts on the mycelial growth of the soil-borne fungal pathogens Pythium sulcatum and Rhizoctonia solani, and the well-known antagonist Trichoderma atroviride. Important differences in their effects were attributed to the level of sinigrin of the two lines; T. atroviride was clearly less sensitive than the two pathogens. Then, an experiment involving successive carrot crops grown in large containers of soil either infested or not infested with R. solani and T. atroviride compared the effects of biofumigation with the same two lines of mustard with bare soil. Although the mustard intercrop was itself attacked by R. solani, results demonstrated that biofumigation provided, whatever the level of sinigrin of the biofumigant crop, an important reduction in soil infectivity over time, as well as reducing the incidence of brown rot disease at the end of the succession. No significant change in the quantity of Rhizoctonia DNA was detected during this period. Moreover, synergy between biofumigation using the high-sinigrin line and T. atroviride was demonstrated. This work supports the hypothesis that biofumigation can operate not only through the short-term direct effects of isothiocyanates (ITCs) on the pathogen but also in the longer-term by altering the balance between pathogens and their antagonists within a modified environment.