Processed cheese has an excellent history of safety; however, it is difficult to eliminate completely fungi and bacterial growth, activity and toxin production that threaten consumer's health. Methods: 120 processed cheese samples were analyzed for determination of total fungi and yeast count, as well as identification of the isolated fungi. Toxicity and aflatoxin produced by the isolated Asp. flavus using thin layer chromatographic technique. Bacillus species and C. perfringens count as spore former organisms. Results: Fungi and yeasts were present in 18 (15%) of processed cheese samples with total count of 2.7x10⁴/g. Asp. flavus was the first prevalent species (55.6%) of the positive samples. 5 (25%) out of 20 isolates of Asp. flavus proved to produce mycotoxins, three of them were able to produce all types of aflatoxins. Mycotoxins producing isolates cause more than 50% mortality of the larvae tested. Some aerobic and anaerobic sporeformers were isolated and counted. B. cereus was isolated from 17 (14.2%) of processed cheese samples with an average count of 7x10²/g.                B. macerans, B. lechniformis and B. megaterium were detected in 8 (6.7%), 20 (16.7%) and 14 (11.7%) of samples, respectively.  Moreover, C. perfringens was present in 16 (13.3%) of samples.  Conclusion: Two important points must be regarded to safe production of processed cheese; first one: is the measures to minimize the presence of spores. The second is to prevent spore germination and vegetative proliferation by adequate cooling during all steps of production till dispensation to the consumers.