The decrease of seed quality during storage is strongly associated with damage caused by free radicals. Some compounds of natural origin, known due to their antioxidative and antifungal properties, may be potentially used in organic production for seed treatment as an alternative to pesticides. The aim of the experiment was to study an ability of hydrogen peroxide and organic acid to improve germination, vigour and health of non-deteriorated and deteriorated zinnia seeds. Two seed samples, cv. Illumination and Orys, varying in initial infestation with fungi were tested. For deterioration seeds were kept at 30°C and 80% RH for 30 days. Seed quality tests were performed before and after deterioration for controls and seeds soaked in 3.0% hydrogen peroxide solution and in 1.0 and 5.0% solutions of ascorbic and lactic acids for 10, 30 and 60 min. The controls were untreated seeds, seeds soaked in 0.2% solution of Kaptan zawiesinowy 50 WP for 30 min and seeds soaked in distilled water for 10, 30 and 60 min. Treating zinnia seeds with organic acids more significantly affected seed germination and health after deterioration than before, and improvement of germination capacity was usually correlated with decrease of the percentage of abnormal diseased seedlings. Deterioration had no influence on mean germination time, whereas in particular cases treating seeds with hydrogen peroxide and organic acids negatively affected this parameter. After deterioration regardless of treatment increased number of seeds free from fungi. Lactic acid followed by hydrogen peroxide and ascorbic acid effectively limited growth of A. alternata, A. zinnia and Fusarium spp. on zinnia seeds, however at higher concentration negatively affected seed germination and vigour. Moreover, treating seeds with hydrogen peroxide and organic acids many a time increased seeds infestation with B. cinerea.