The difficulty on identifying, lack of segregation systems and absence of suitable standards for coexistence of non trangenic and transgenic soybean are contributing for contaminations that occur during productive system. The objective of this study was to evaluate the efficiency of two methods for detecting mixtures of seeds genetically modified (GM) into samples of non-GM soybean, in a way that seed lots can be assessed within the standards established by seed legislation. Two sizes of soybean samples (200 and 400 seeds), cv. BRSMG 810C (non-GM) and BRSMG 850GRR (GM), were assessed with four contamination levels (addition of GM seeds, for obtaining 0.0%, 0.5%, 1.0%, and 1.5% contamination), and two detection methods: immunoassay of lateral flux (ILF) and bioassay (pre-imbibition into 0.6% herbicide solution; 25 ºC; 16 h). The bioassay is efficient in detecting presence of GM seeds in seed samples of non-GM soybean, even for contamination lower than 1.0%, provided that seeds have high physiological quality. The ILF was positive, detecting the presence of target protein in contaminated samples, indicating test effectiveness. There was significant correlation between the two detection methods (r = 0.82; p < 0.0001). Sample size did not influence efficiency of the two methods in detecting presence of GM seeds.