Bassi preceded Louis Pasteur in the discovery that microorganisms can be the cause of disease (the germ theory of disease). He discovered that the muscardine disease of silkworms--a disease that was destroying the silk industry--was caused by a living, very small, parasitic organism, a fungus that would be named eventually Beauveria bassiana in his honor. To cure and prevent the disease Bassini recommended the use of disinfectants, separating the rows of feeding caterpillars, isolating and destroying infected caterpillars, and keeping the farms clean.

In demonstrating the parasitic nature of the muscardine disease of silkworms, Bassi also founded the doctrine of pathogenic microorganisms. His ideas inspired Henle (1840; No. 2533).