Sorghum serves as staple food for over 100 million people in Sub-Saharan African countries. It is the most important nutritional security crop and ranks third among major cereal crops in terms of area and production next to teff and maize in Ethiopia. However, Sorghum is susceptible to contamination by molds that produces aflatoxin that causes hepatotoxic and carcinogenic effects on humans and animals. This study was conducted to assess Aspergillus species and aflatoxin level in Sorghum (Sorghum bicolor L.) stored under different storage system for different storage period. Thirty samples were analyzed for aflatoxin contamination using high performance liquid chromatography equipped with fluorescent detector and Aspergillus species were isolated and identified using phenotypic features in a potato dextrose agar culture media. About 56.7%, 16.7%, and 23.3% of the Sorghum samples were found to be contaminated with Aspergillus flavus, Aspergillus niger and Aspergillus parasiticus, respectively. The level of total aflatoxin, aflatoxin B1, aflatoxin B2, aflatoxin G1, and aflatoxin G2 were in the range of 11.44 to 344.26µg/kg, 3.95 to 153.72µg/kg, 1.17 to 91.82µg/ kg, 9.87 to 139.64µg/kg, and 3.22 to 52.02µg/kg, respectively. The concentration of aflatoxin in all Sorghum samples surpassed the maximum level set by the European commission and therefore, deserves attention to control them across the Sorghum value-chain. Keywords: Aflatoxin; Aspergillus species; Sorghum; Storage Period; Storage System Citation: Weledesemayat GT, Gezmu TB, Woldegiorgis AZ, Gemede HF (2016) Kewet woreda is one of the Sorghum producing districts in the country and farmers use both underground pit and above ground storage systems. The storage system "Gotera" are made from different plants, clay, grass, ash, and cow dung. In the underground pit storage, they wash the pit with water and put the Sorghum grain until they are full, then the cover with grass, clay and flatted stone. Some farmers are using cleaning, insecticides and fumigants to prevent insect damage and adding the Sorghum grain in to the pits. The grain is stored for long periods; especially, this is the case during times of food scarcity. These storage systems are believed to protect against insect damage and theft, fire, domestic and wild animals and improve the quality of Sorghum as well. These Sorghum grains are stored under unhygienic conditions and very often spoiled by moulds and may develop mycotoxin contamination. Therefore, this particular research was endeavored to analyze the occurrence of Aspergillus species and aflatoxin content in Sorghum grain stored at different time periods and different storage system.