Studies were conducted in 2001 to determine the effect of transgenes on mean performance and stability of selected cotton cultivars for a variety of non-target traits. Multi-environment trials are conducted every year and mean performance is often calculated as an average of cultivar performance over years and locations. However, comparisons of mean performance are not sufficient for cultivar evaluation without an understanding of the causes of genotype x environment (GE) interactions. A graphical data summary called GGE Biplot can be used to characterize GE interactions and make meaningful comparisons between cultivars. A multi-environment data set was used with GGE Biplot to compare conventional and transgenic cotton cultivars. Preliminary analyses of variance (ANOVA) in SAS revealed that GE interactions were present only for plant height, number of nodes, fuzzy seed index, and lint percent. There were no GE interactions for yield. Plant height at 60 DAP, fuzzy seed index, and lint percent were analyzed in GGE Biplot, and differences, based on environment, between conventional and transgenic cultivars were further examined. Transgenic and conventional cultivars did not behave similarly for plant height, fuzzy seed index, or lint percent at the four locations in this study. The relative differences between transgenic plants and their conventional counterpart differed based on environment and crossover interactions were present. Additionally, transgenic plants were taller, and their seed were heavier than conventional plants, although the degree of which these differences were present was dependent on location. In all cases, conventional plants had higher lint percentages than transgenic plants.