An epitope is that part of an antigen that is recognized by the immune system, more specifically by antibodies, B cells, or T cells.  An epitope is a relatively a short sequence of amino acids and a typical full-length protein contains many different epitopes against which antibodies can bind.  The part of an antibody that binds to the epitope is called a paratope.
 The immune system is divided into innate and adaptive categories. Innate immunity involves nonspecific defence mechanisms that act immediately or within hours after microbial invasion.  Adaptive immunity is only present in vertebrates and is highly specific.  The adaptive immune system recognises and destroys invading pathogens individually and remembers the pathogens, a process mediated by T- and B-cells.  These cells do not recognize pathogens as a whole, but instead recognize epitopes within them.  Epitopes, which is a term which can be used interchangeably with antigenic sites or antigenic determinants, can be classified as B cell epitopes or T cell epitopes on the basis of the types of cellular response they elicit.
Identifying epitopes in antigens allows better understanding of disease etiology, immune monitoring, the developing of diagnosis assays, and the design of epitope-based vaccines.

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