Cadmium (Cd) stress may cause serious physiological, ultramorphological and biochemical anomalies in plants. Cd-induced physiological, subcellular and metabolic alterations in two transgenic cotton cultivars (BR001, GK30) and their parent line (Coker 312) were evaluated using 10, 100 and 1000 µM Cd. Germination, fresh biomass of roots, stems and leaves were significantly inhibited at 1000 µM Cd. Root volume tolerance index significantly increased (124.16%) in Coker 312 at 1000 µM Cd. In non-Cd stressed conditions, electron micrographs showed well-configured root meristem and leaf mesophyll cells. At 1000 µM Cd, greater ultramorphological alterations were observed in BR001 followed by GK30 and Coker 312. These changes were observed in nucleus, vacuoles, mitochondria and chloroplast. Dense precipitates, probably Cd, were seen in vacuoles, which were also attached to the cell walls. A considerable increase in number of nuclei, vacuoles, starch granules and plastoglobuli was observed in the electron micrographs of both roots and leaves at 1000 µM Cd. MDA contents were higher in roots of BR001 at 1000 µM Cd. Mean values of SOD activity in leaves of both BR001 and GK30 at 1000 µM Cd significantly increased as compared to the controls. POD activity in roots of BR001 and Coker 312 was greater at all Cd (10, 100, 1000 µM) levels over the control. Regarding APX, highest percent increase (71.64%) in roots of GK30 at 1000 µM Cd was found. Non-significant differences in CAT activity were observed at all levels of Cd stress in leaves of BR001 and GK30. Both transgenic cotton cultivars and their parental line invariably responded towards Cd stress. However, Coker 312 showed Cd-resistant behavior as compared to its progeny lines (BR001 and GK30).