Ten fungi associated with four sunflower seed genotypes (Sakha53, Giza102, L92 and L120) were isolated and identified. These fungi were Alternaria alternata (Fries) Keissler, Aspergillus flavus Link, Aspergillus niger V. Tiegh, Aspergillus sp., Cladosporium herbarum (Perssen) Link, Fusarium equestii (Corda) Saccardo, Humicola grisea Traaen, Paecilomyces variotii Bainier, Penicillium sp. and Rhizopus oryzae Went and Prinsen. The highest percentage of A. flavus infection was noticed with seeds of sunflower genotype L120 at two years after storage. The presence of aflatoxin was determined in contaminated sunflower seeds using HPLC methods. Four genotypes sunflower seeds were stored for two years with aflatoxin contamination except L92 genotype seeds. Increasing storage duration led to significant gradual decrease in seed oil and in fatty acids i.e. oleic and linoleic which associated with increasing moisture content. Significant differences were found among the tested sunflower genotypes, seed storage durations and their interaction for percentage germination, seed yield and its components under field conditions. The genotype L92 had the best storability which gave the highest percentage values of field germination and seed yield/fad., at field experiments as combined data over locations. Increasing storage durations caused relatively large reductions in yield and its components. The effective interacting treatment gave the highest seed yield/fad when genotype L92 was sown without storage (pre storage), since its yield remained high with increasing storage durations till two years after storage compared with other ones.