Purpose: The objective of this study was to investigate the physicochemical characteristics of seeds oil extracted, roots and leafs from genetically modified cotton seeds and local non-genetically modified.
 Methodology: Cotton seeds samples were collected from Elguziera State farms and White Nile State farms, Sudan. Collected samples were transferred to the Central research laboratory of natural and environmental resources. Oil from cotton seeds was extracted using soxhlet method, hexan was used as solvent. Determined physicochemical characteristics were pH, refractive index, specific gravity, free fatty acids, acid value, peroxide value, iodine value, saponification value, and In addition the moisture, ash, protein, fat, fiber, calcium, Iron, magnesium, Potassium, and phosphor from roots and leafs.
 Findings: The two oil samples showed significantly (P≤0.05) difference in oil content, but they showed no significant difference in refractive index with a mean value of 1.47, also specific gravity; in all samples ,had value (0.94), showed significantly (P≤0.05) difference in peroxide values between Elguziera State farms and White Nile State farms; also significant (P≤0.05) difference in iodine value (7.61, 1.67, 2.18 and 1.167 respectively) was observed, saponification value (5.61,1.96, 1.96,and 4.77 respectively), free fatty acids (2.82,1.80,3.03 and 8.84 respectively), acid value (4.20,4.48,4.48 and 4.76, respectively) showed significant (P≤0.05) difference.