A study was conducted to determine whether stand densities of transgenic cotton (Gossypium hirsutum) varieties, with or without glyphosate, were similar to conventional varieties of the same lineage group in Georgia and Mississippi. Transgenic and conventional cotton varieties were placed into five lineage groups of related varieties and seedling disease was evaluated in three greenhouse tests and a field trial using Rhizoctonia solani AG-4. Seed vigor was determined by standard germination studies were conducted evaluating conventional and transgenic varieties of similar lineage. Results showed that no interactions occurred for the heights and dry weight data across treatments within the lineage groups in any of the experiments. No interactions were shown between stand densities at different inoculum rates and inoculated versus uninoculated pots (plots). Across all greenhouse studies, stand counts of PM 1220 were similar to the transgenic varieties PM 1220 RR and PM 1220 B/RR with or without a glyphosate application. In the field trial, PM 1220 B/RR + glyphosate had significantly lower stands than all other treatments expect PM 1220 RR (no glyphosate treatment) prior to and after glyphosate application. Stand densities for varieties within the lineage group DPL 5415 were also inconsistent when compared between the greenhouse and field trials with no apparent trends occurring. However, the Coker 312 varieties containing glyphosate tolerance had consistently lower stand counts compared to the conventional variety of Coker 312 but only during the greenhouse studies. Seed germination of Coker 312 could not be correlated with either the greenhouse or field trial data. In general, the commercially available varieties such as PM 1220, DPL 5690, DPL 5415, and DPL 50 with glyphosate tolerance had similar stand count, height, and dry weight data when compared to the conventional varieties from the same lineage group regardless of a glyphosate application. When differences did occur, no consistent trends could be determined within these four lineage groups.