In present investigation, toxic effect of secondary metabolites secreted by rhizospheric fungi isolated from Bt-cotton against seed germination and seedling growth was tested in Wheat and Jowar. The culture filtrate of Penicillium islandicum, Trichoderma viride, Aspergillus niger, Fusarium oxysporum and Alternaria solani was obtained. Seed germination percentage and growth was affected by all five fungal secondary metabolites. The secondary metabolites of Trichoderma viride and Penicillium islandicum enhances seed germination percentage while it was least by Aspergillus niger, Fusarium oxysporum and Alternaria solani.