Antigen molecular mimicry Let us consider a situation in which the body is attacked by a microbe, and the microbe is captured by the immune system for recognition of surface antigens. The surface antigen recognized mimics one of our self antigens. It is stated in textbooks that this situation results in the immune system attacking the microbe along with the tissue containing the self antigen(auto-immunity). (Reference: Robbins and Cotran pathologic basis of disease) If a microbial antigen mimicks self antigen, why is the microbial antigen attacked instead of being ignored in the way that all our self antigens are ignored by our immune system?

There are different type of immune cells which falls under either **innate** or **adaptive system**.

The cells under the innate are first to respond microbial attack and are able to detect them in extracellular environment by recognizing proteins/peptides called **Pathogen-associated Molecular Patterns (PAMPs)** on their surfaces; these are only found on microbes.

But when the innate system fails to clear the microbes in time, the adaptive system is kicked-in. This involves T-lymphocytes and B-lymphocytes. T-lymphocytes are trained to ignore cells that are able demonstrated that they self but B-lymphocytes which produces **antibodies/immunoglobulins** to the detected antigens do not have a mechanism of ignoring self cells.

So the problem lies with when the immune response gets to the point where antibodies are produced, at that point produced antibodies simply attack without discrimination.

I hope this simplified version would help you.