The presence of a charged hydrophilic head group makes a detergent ionic. Ionic detergents can be either anionic (negatively charged) or cationic (positively charged).

Ionic detergents have a much stronger effect as compared to nonionic detergents. This is because they bind to protein molecules, altering the structure and charge of the protein. Ionic detergents are often used when the preferred outcome involves the total breakdown of cellular structures and denaturing of proteins for separation during gel electrophoresis.