The chemical composition and natural occurrence of mold and mycotoxins contamination in whole cottonseeds and their meals were carried out for six Egyptian cotton cultivars (Giza 45, Giza 70, Giza 86, Giza 85, Giza 80 and Giza 89). The results showed that there were differences between the varieties. Since both the cottonseed meal and cottonseed-oil were found to be free of any mycotoxins for all the varieties, so they are safe for the health of both human and animal. The relationship between moisture ⁰/0 and natural occurrence of zeralenone showed significant positive correlation, also between protein % and aflatoxin contamination. While there was a high significant negative correlation between total fungal count and protein % and between oil % and natural occurrence of aflatoxins. Giza 70 variety exhibited special behavior, it attained the highest content for moisture and gossypol among all cottonseeds and their meals, and the highest protein content for cottonseed meal. It also had the lowest total fungal count.