Cotton is widely acknowledged as a major cash crop across the world, and its socioeconomic relevance, particularly in emerging nations, is well understood. Cotton seedling infections are among the most significant of the diseases that limit cotton lint and seed production. The goal of this study was to determine the pathogenicity of Rhizoctonia solani, Fusarium moniliforme, and Machrophomina phaseolina isolates taken from cotton roots to cotton seedlings in the Giza governorate. Seven fungus isolates were recovered from two cotton cultivars, including Rhizoctonia solani, F. moniliforme, and M. phaseolina (Giza 90 and Giza 94). It was discovered that the differences in pathogenicity between the isolates and controls vary by cultivar, indicating that the cultivars reacted differently to the isolates. All of the fungal isolates were harmful and reduced the survival rate on both cultivars. Pathogenic isolates had a negative impact on seed germination, root shoot length, and increased Cotton seedlings have a significant mortality rate. These problems might be overcome by growing cotton cultivars that are resistant to damping-off. In order to improve resistance, resistance genes must be introduced into cotton cultivars. Future cotton improvement techniques should incorporate damping-off management; however, the inclusion of numerous pathogenic fungi from various genera may confound efforts to create such approaches.