The transgenic and non-transgenic soybean seeds oils were extracted and the composition and concentration of the fatty acids were analyzed by gas chromatography. Sixteen different fatty acids were detected in both transgenic and non-transgenic soybean oil: C14:0, C16:0, C18:1, C18:2, C18:3, C20:0, C20:1, C20:2, C22:0, C20:5, C22:1, C24:0 and C22:6. The concentration of 12 of 16 fatty acids (C14:0, C16:0, C18:1, C18:2, C20:0, C20:1, C20:2, C22:0, C20:5, C22:1, C24:0 and C22:6) in transgenic soybean oil were higher than those in non-transgenic one (P < 0.05). The concentration of C17:0 and C18:3 were lower than those in non-transgenic one (P < 0.05). The total fatty acids concentration increases by 12.6 % (P < 0.01). The degree of saturation of transgenic soybean oil increased from 58.7 to 69.8 % (P < 0.01). All the data above show that the insertion of foreign genes can change the concentration of fatty acids in plant oil. The mechanism for these changes should be studied.