An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The part of an antibody that recognizes the epitope is called a paratope. Although epitopes are usually thought to be derived from non-self proteins, sequences derived from the host that can be recognized are also classified as epitopes. Usually five to eight amino acids are critically involved in determining an epitope although many more actually interract with the antigen binding site of the antibody.  Understanding these protein epitopes is important for the design of vaccines, adjuvants, and the clinical use of therapeutic proteins.

The epitopes of protein antigens are divided into two categories, conformational epitopes and linear epitopes, based on their structure and interaction with the paratope. A conformational epitope is composed of discontinuous sections of the antigen's amino acid sequence. These epitopes interact with the paratope based on the 3-D surface features and shape or tertiary structure of the antigen. Most epitopes are conformational.

In contrast linear epitopes interact with the paratope based on their primary structure. The amino acids that make up a linear epitope are a continuous sequence of amino acids from the antigen.