Seed quality is crucial for a satisfactory crop establishment. It is also an important part of the process of breeding for sustainable farming systems, where varieties often grow under more difficult conditions than in conventional farming systems. Previous research suggests that corn genotypes and the environment where seeds are produced have an effect on seed quality. The objective of this study was to determine seed quality differences between organic and conventional farming systems. Twenty high protein breeding genotypes derived from exotic by adapted crosses were planted during two growing seasons in conventional and organic nurseries near Ames, Iowa, to produce seeds for laboratory tests. The laboratory tests to assess germination and vigor included: standard germination, saturated cold test, accelerated aging and soak test. Complementary tests such as fast green and electrical conductivity were performed to assess mechanical damage and membrane integrity of seeds, respectively. Protein and oil compositions also were analyzed by NIR. The standard germination and saturated cold test indicated that genotype and environment where seeds were produced affected seed quality. The germination and saturated cold test percentages of seeds produced in the organic farming system were lower than for seeds produced in the conventional system. The interactions between location and genotype was non significant in 2003 and 2004. These results indicate that selection of high seed quality genotypes for the organic system can be accomplished in the conventional system. Genotype also influences the protein and oil content of the seed. Protein was unaffected by the production environment, but oil content depended on environment. The oil content of seeds produced in the organic system was significantly higher than in the conventional system. This is important when selecting high protein lines in a conventional system as protein content will remain high when lines are grown in the organic farming system.