Hypocotyl lengths have been measured previously as a means of comparing early seedling growth, but not under field conditions. Since the hypocotyl comprises a significant portion of the total shoot height until about 1 month after planting, visual ratings of seedling vigor could potentially be influenced by hypocotyl length, and therefore by the height of the seedlings. On-farm, large-plot field trials were established across the Mid-South and Southeast regions in 2000 and 2001 to determine if hypocotyl length differs among varieties, and to determine if hypocotyl length, seedling vigor ratings, and lint yields are related. Seedling vigor ratings and hypocotyl lengths were recorded at fourth true leaf stage, as well as lint yield at the end of the season. The length of hypocotyl on cotton seedlings significantly differed for early-maturing and full-season Bollgard^®/Roundup Ready^® varieties in the study, but did not differ for the Roundup Ready^® varieties in the study. Seedling vigor ratings differed among varieties in all data sets except full-season Roundup Ready^® varieties. The length of the hypocotyl was significantly, though weakly, associated with seedling vigor ratings, suggesting that hypocotyl length may be inadvertently and partially included within breeders’ selection for higher seedling vigor. Results from this study suggest that hypocotyl length may be a more reliable method of measuring early seedling vigor versus using visual ratings; however, the time required to measure hypocotyl length versus using a visual rating may deter its use in a commercial breeding program. Lint yield was not associated with either hypocotyl length or seedling vigor, which supports previous work.