The 2006 National Cottonseed Treatment Program evaluated cotton seedling survival for a number of fungicide seed treatment combinations over diverse environmental conditions and levels and types of cotton seedling pathogens. Twelve fungicide seed treatments were nominated by chemical industry representatives for evaluation in the 2006 National Cottonseed Treatment Program. A standard fungicide treatment, Vitavax-PCNB + Allegiance, and a nontreated control were included to assess efficacy of the nominations and seedling disease pressure. In addition, the fungicide treatments Allegiance or PCNB were included to aid in determining the importance of Pythium spp. or Rhizoctonia solani, respectively. Disease ratings and pathogen isolations for seedlings and soil populations of selected soilborne genera were conducted by collecting seedlings and soil from the nontreated control plots at each location. Soil temperature and water and plant development data also were collected for sites for the 2006 National Cottonseed Treatment Program.