The seedling disease complex causes damage to seed and seedlings wherever cotton is grown. Factors contributing to its complexity involve: the status of seed and seedling traits that may lead to problems due to predisposition; the seed may rot or its performance may be impaired; the seedling hypocotyl and/or primary and secondary roots may be destroyed or only damaged sufficiently to impair performance; and several primary and, under conditions of predisposition, secondary pathogens may individually or in combinations cause damage. Exposure of seed naturally or under management during crop maturation, harvesting or processing to excessive periods of moisture and heat predisposes seed to rotting organisms and seedlings to damage by secondary pathogens. Predisposition can be sufficient to cause loss of resistance in seed and seedlings to pathogens. The seed coat, radicle, hypocotyl, primary and secon dary roots are each distinct tissues that respond differently to predisposition and attack by pathogens. The primary pathogens functioning singularly or in combinations may be Rhizoctonia solani Kuehn, Pythium spp., Thielaviopsis basicola (Berk. & Br.) Ferr. and Glomerella gossypii Edg. The secondary pathogens such as bacteria, Fusarium spp., Aspergillus spp., Rhizopus spp. and Alternaria spp. attack predisposed seed and seedlings. All of these a facets of seed, seedlings and pathogens must be considered in dealing with genetic improvement and crop management to reduce seedling disease losses.