A two-season (2003 and 2004) greenhouse study conducted to study the effect of cotton seed treatment with the insecticide Gaucho on the efficiency of the fungicide Monceren in controlling seedling disease. Thus 4 treatments were evaluated on seven Egyptian cotton cultivars (Giza 80, 83, 85, 86, 88, 89, and 90). The treatments were: seed treated with Monceren and Gaucho, seed treated with Monceren, seed treated with Gaucho, and untreated control. In 2003, cotton cultivar and treatment were highly sources of variation on pre-emergence damping-off, while their interaction was significant source of variation. Treatment was the only significant source of variation on the incidence of postemergence damping-off. Both cultivar and treatment were highly significant sources of variation on survival. All sources of variation were nonsignificant sources of variation on dry weight of seedlings. In 2004, cultivar and treatment were highly significant sources of variation on incidence of preemergence damping-off but their interaction was nonsignificant sources of variation. All source of variation were nonsignificant on postemergence damping-off. Cotton cultivar was a highly significant source of variation on survival and the treatment was significant source. The interaction between cultivar and treatment was nonsignificant. Regarding the dry weight, treatment was the only significant source of variation. In 2003, thirteen fungal genera were isolated from roots of seedlings of different treatments. These genera were: Fusarium, Rhizoctonia, Penicillium, Aspergillus, Alternaria, Stemphylium, Rhizopus, Chaetomium, unknown sterile isolate, unknown sporulated isolate, Helminthosporium, Trichoderma, and Cladosporium. In 2004, nine fungal genera were isolated from seedlings of different treatments. These genera included: Fusarium, Rhizoctonia, Penicillium, Alternaria, Aspergillus, Nigrospora, Trichoderma, Chaetomium, and Phoma. In each year, effects of treatments on isolation frequency of fungi was evalulated. The correlation between isolation fraquancy of fungi and seedling disease variables was also evaluated.