The present work was developed in the laboratories of Seed Analysis and Seed Pathology at the Universidade Federal de Lavras, with the purpose of screening soluble protein extracting buffers and isozyme systems to detect variations in electrophoretical patter in corn seeds with different levels of deterioration. Two seeds lots of the cultivars AG-122 and C-901 were artificially aged for different periods. After ageing, the seeds had their profile determined by physical, physiological and sanitary (health) tests. The results obtained revealed that the electrophoretical variations of proteins and isoenzymes are associated with the deteriorative process of corn seeds. The extractor Hepes offers better resolution in the evaluation of the level of deterioration of seeds. The enzymes glutamate-oxalacethate transaminase and sorbitol dehydrogenase may be considered promising biochemical markers for evaluating the quality of corn seeds in early deterioration stages.