The fungus Sclerotinia sclerotiorum, the causal agent of white mold, is widespread throughout the world. The disease is considered to be one of the major diseases of soybean and bean crops in Brazil. The pathogen S. sclerotiorum is spread by soybean and bean seeds both in the form of sclerotia and dormant mycelium inside the seeds. The objective of this work was to evaluate the relationship between different potentials of S. sclerotiorum in soybean and bean seeds and the performance of these seeds, as well as to verify the localization and quantification of the inoculum of the pathogen in the seeds inoculated by Real-time PCR (qPCR), validating the term inoculum potential. Soybean and bean seeds were inoculated with the fungus by the osmotic conditioning method based on the exposure of the seeds to the fungus for periods of 24 h, 48 h, 72 h, and 96 h. Molecular analysis was carried out by means of qPCR in whole seeds and dissected in the integument, cotyledon and embryonic axis. The results showed that the effects of S. sclerotiorum on seed germination and vigor were progressive and proportional to the increases in inoculum potentials, since there was more severe damage to the seeds and consequently to the emerged plants at the highest potential (P96). The inoculum of the pathogen was found in all parts of the evaluated seeds, even at its lowest inoculum potential (P24), with an increasing DNA concentration, and the integument obtained a greater amount of DNA than the embryo, in comparison.