Surface and non-surface sterilized seeds of commercial cotton cultivars were examined for qualitative and quantitative estimates of seed-borne fungi. Aspergilus flavus, A.niger  and Alternaria alternata were the most dominant species isolated. Cultivar and cultivar treatment interactions were very highly significant source of variation in frequencies of fungi. Both cultivar and  cultivar x treatment interactions contributed most to the variation in frequencies of the isolated fungi. The effect of surface sterilization on frequencies of fungi isolated from seeds varied depending on the cultivar used. Giza 85 cultivar yielded the lowest number of fungi (5 fungi). Other cultivars yielded a number of fungi ranging from 7 to 13. The role of seed borne fungi in cotton seedling disease incidence was more evident in the post-emergence stage compared with the pre-emergence stage. Also, Cluster analysis divided the cotton cultivars into two distinct groups, one group consisting of 6 cultivars (Giza 45,Giza 70,Giza 85,Giza88,Giza89 and Giza90) and a second group consisting only one cultivar Giza90.Constructed regression models showed that difference in seedling disease variables were due largely to the effects  of  A. alternata, Cladosporium spp. and Fusarium semitectum .