The suitable establishment of a crop depends on seed quality, among another factors. However, with high production costs many producers use uncertified seeds, to reduce expenses with this input at sowing time. The objective was to evaluate germination, vigor and health of soybean seeds, diseases incidence in cvs. NS 5445 IPRO and BMX Ativa RR, whose seeds were of certified and uncertified origins, as well as yield components and grain yield of soybeans, with or without fungicides application. The experiments were conducted in the 2015/16 and 2016/17 crop season, in Erechim-RS. Two experiments were carried out in a completely randomized design (DIC): one in the laboratory, under a 2 x 2 factorial scheme (cultivar x origin); and another in the field in a homogeneous area, in a 2 x 2 factorial scheme (with/without fungicide application and certified/uncertified seed) for two cultivars, both with four replications. The variables evaluated were: germination and seed health, yield (kg ha-1), thousand grains weight (g), number of grains per plant, and incidence of foliar fungal diseases. The main fungi identified in seeds were Aspergillus sp., Penicillium sp. and Fusarium sp. The highest incidence percentage were obtained in uncertifed seeds, at two harvests. Both cultivars and origins presented the minimum germination required for commercialization, however, certified seeds had better performance for seed vigor. As for normal seedlings, there was a significant difference only for the 2016/17 crop season, with the highest percentage obtained in certified seeds (52.0% for NS 5445 and 73.5% for BMX Ativa). Best productivity was achieved with cultivation of certified seeds associated with fungicides in both crops and cultivars. For thousand grains weight (TGW) there was no difference in origin, but only for cultivar and fungicides apply. The number of grains per plant was higher in plants from certified seeds and that received fungicides, being cv. BMX Ativa the most responsive for the two harvests analyzed. The main diseases found in the two harvests were: Asian rust, powdery mildew, mildew, septoriosis and cercosporiosis. However, seed origin, in both crops, did not differ in the incidence of Asian rust, powdery mildew and mildew, but for septoriosis and cercosporiosis, considered soybean late season diseases, seed origin is a determining fator.