Laboratory experiments were conducted to evaluate the effects of storage containers (aluminum foil bag, polythene bag, plastic container, metal container and earthen pot), seed moisture level (5, 7, and 9%) and storage conditions (ambient temperature 30 ± 2o C, refrigerator 8 ± 1o C and dehumidified condition 20o C and RH at 40%) on germination and prevalence of seed-borne fungi of onion seed over a period of 170 days. Among the storage containers aluminum foil bag, polythene bag and plastic container performed better on germination and prevalence of seed-borne fungi of seeds. Seeds maintained high germination and lower seed-borne fungi when stored with 5 and 7% initial moisture. Considering storage conditions, refrigerator and dehumidified storage performed better. In two way interaction of container and seed moisture level, the highest germination and lowest seed-borne fungal infection was recorded in seeds stored in aluminum foil bag with 7% moisture content. In case of storage container and storage condition the highest germination and lowest prevalence of seed-borne fungi was recorded in seeds stored in aluminum foil bag in refrigerator, while in moisture level and storage condition better quality was maintained in seeds with 7% moisture level stored in refrigerator. From the results of the present experiment, it is suggested that onion seeds may be stored in sealed container and cool condition. The initial moisture content of seed should also be minimum (5 to 7%) for maintaining good quality and health of onion seeds.