Periodic stand establishment problems have raised concerns about the relative occurrence and severity of the seedling disease complex in transgenic and conventional cotton cultivars. This study was undertaken to compare stand establishment parameters among transgenic and conventional cotton cultivars within selected family lineages. Greenhouse and field tests were conducted in Georgia and/or Mississippi on transgenic and conventional cotton cultivars and breeding lines of DP 5690, DP 5415, DP 50, PM 1220 and Coker 312. Significant differences in seedling survival between conventional and transgenic entries within family lineages were rare. Those that occurred did not appear related to the presence or absence of Roundup Ready^®, cry1Ac or cry2Ab genes. There were no significant differences in hypocotyl disease index, root disease index or yield among transgenic and conventional entries from DP 5415 and DP 50 family lineages.