Experiments were carried out at Rice Research and TrainingCenter during 2004 growing season and storage period from October 2004 to March 2006. The study aimed to investigate the effect of grain storage periods with different levels of nitrogen fertilization (0, 23, 46 and 69 Kg N/ fed.) or storage moisture content of 14, 16, 18 and 20 % on discolored grains, fungal association and seed germination. The results showed that percentage of discolored grain and fungal association with rice grains increased by increasing storage periods regardless to the moisture content. On the other hand, seed germination decreased with the increase of storage period. Two types of bags were used to store the grains (striped plastic and jute sacks). The percentage of grain discoloration and associated fungi increased in striped plastic than in the jute sacks. The discoloration percentage and associated fungi on stored grains increased under 0 and 69 compared with 46 or 23 nitrogen levels. Giza 177 was the most affected cultivar with previous nitrogen levels, followed by Sakha 101, while, Giza 178 was the least one. Concerning the effect of rice grain moisture content with storage period on rice cultivars, data showed that the discoloration percentage increased with increasing of grain moisture content, while the germination percentage decreased. Giza177 and Sakha 104 were the most affected cultivars showing the highest discoloration percentage, associating fungi and the least germination. Alternaria spp, Bipolaris oryzae and Fusarium spp, were the most common fungi on grains before storage, while after 16 months of storage, the common fungi were Aspergillus spp and Penicillium spp. Presence of Rhizopus spp was the least one. In the greenhouse, eleven fungi were used for artificial inoculation on Giza 177. Bipolaris oryzae induced the highest grain discoloration (58.6 %) followed by Alternaria padwickii. and Curvularia lunata with 51.3 and 48.2 %, respectively. While Aspergillus spp and Penicillium spp. and un-inoculated pots showed the least grain discoloration with 2.2, 1.9 and 1.5 %, respectively.