Isotype and allotype are terms that relate to the structure of a component of the immune system that is called an immunoglobulin.

Immunoglobulins bind their corresponding antigen. An immunoglobulin can be static, as part of a membrane-bound receptor to which an antigen binds, or can be floating freely in the body as an antibody. The antigen-binding capacity of an immunoglobulin is related to the three-dimensional shape of the molecule. Immunoglobulin isotype and allotype determines the diversity in shape of immunoglobulins.

Immunoglobulins are structured with two Y-shaped "heavy" chains. To each of these a shorter "light" chain is linked. Within each chain there are regions whose amino acid sequence remains constant from immunoglobulin to immunoglobulin. There are also regions whose amino acid sequence is somewhat different and markedly different between the myriad of immunoglobulins that can be made.

The type of heavy chain an immunoglobulin has determines the isotype. Immunoglobulins of the same isotype have the same amino acid structure in two specific regions of the heavy chain. The similarity in amino acid sequence extends to the three-dimensional structure that the immunoglobulin adopts. Thus, immunoglobulins of the same isotype have similar shapes and so similar antigen binding characteristics. The different classes and subclasses of antibody protein arising from the amino acid variations represent the different isotypes.

In humans, there are five immunoglobulin isotypes: IgA, IgD, IgG, IgE, and IgM. All humans whose immune system is functioning correctly possess all these isotypes. Thus, no antigenic response would be elicited if an IgA from one person was injected into another.

Immunoglobulins can also be classified by their so-called allotypes. Allotypes are also determined by the amino acid sequences of the heavy and light chains. Allotypes focus on the variable regions of the chains. By their variable nature, differences in the amino acid sequence can exist even between members of the same species. Allotypes represent what is termed polymorphisms within certain heavy or light chains.

Not all members of a species such as man possess any particular allotype. In contrast to isotypes, the injection of a specific allotype from one person into another could elicit an antigenic reaction in the recipient.