The objective of this study was to evaluate the physiological quality of seeds from conventional (cultivar CD 216) and transgenic (cultivar CD 212RR) soybeans treated with glyphosate. Seeds were soaked in dosages of zero; 1.8; 3.6; 5.4 and 7.2 g.L-1 of acid equivalent of glyphosate for 30 minutes. Seed quality was evaluated from the tests of first count germination, germination, electrical conductivity, emergence speed index, seedling emergence, root and shoot length and total dry matter. It was concluded that the physiological quality of the CD 212RR seeds is affected by glyphosate and as dosages increased, soybean seed quality decreased. Based on this conclusion, it is important that care be taken to avoid problems with seed germination and soybean field establishment when glyphosate is used in burndown or for the control of cover crops. A certain period of time between the control of weeds or of cover plants should be respected to reduce the glyphosate transfer from target to non-target plants, thus avoiding problems with germination and soybean crop establishment.