This study looks at the effects of different manure storage systems and how pathogens survive in each different system. Methods were developed to sample and analyses the manure. Several different storage systems and manure types were reviewed, and they were: dairy and swine liquid manures, dairy solid, poultry solid, and beef solid. For each type typical and modified methods were compared. For liquid manure, storage without fresh manure additions appeared to reduce some of the pathogens. Results from the dairy solid trials indicated that storage of calf manure separate from the milking herd manure resulted in a much greater degree of pathogen decline. The poultry manure composeted very quickly to the point that E.coli was below detection level. Pathogen decline in the solid beef manure piles appeared to be greater in covered piles, but the results varied depending on locations of the piles.