Knowledge of the vertical and horizontal distribution of Aphis gossypii Glover (Hemiptera: Aphididae) on genetically modified cotton plants over time could help optimize decision-making in integrated cotton aphid management programs. Therefore, the aim of the present study was to determine the vertical and horizontal distribution of A. gossypii in non-transgenic Bt cotton and transgenic Bt-cotton over time during two cotton seasons by examining plants throughout the seasons. There was no significant interaction between years and cotton cultivar treatments for apterous or alate aphids. Considering year-to-year data, analyses on season-long averages of apterous or alate aphids showed that aphid densities per plant did not differ among years. The number of apterous aphids found per plant for the Bt transgenic cultivar (2427 apterous aphids per plant) was lower than for its isoline (3335 apterous aphids per plant). The number of alate aphids found per plant on the Bt transgenic cultivar (12.28 alate aphids per plant) was lower than for the isoline (140.56 alate aphids per plant). With regard to the vertical distribution of apterous aphids or alate aphids, there were interactions between cotton cultivar, plant age and plant region. We conclude that in comparison to non-Bt cotton (DP 4049), Bt cotton (DP 404 BG (Bollgard)) has significant effects on the vertical, horizontal, spatial and temporal distribution patterns of A. gossypii, showing changes in its distribution behaviour inside the plant as the cotton crop develops. The results of our study are relevant for understanding the vertical and horizontal distribution of A. gossypii on Bt cotton cultivar (DP 404 BG (Bollgard)) and on its isoline (DP 4049), and could be useful in decision-making, implementing controls and determining the timing of population peaks of this insect.