The hydrophobic effect is the property that nonpolar molecules like to self-associate in the presence of aqueous solution. In the most extreme case, oils will pool together and fail to be miscible with water; detergents forming micelles and bilayers (as in soap bubbles) are another dramatic consequence of the hydrophobic effect.

The hydrophobic effect is usually described in the context of protein folding, protein-protein interactions, nucleic acid structure, and protein-small molecule interactions.

In the case of protein folding, it is used to explain why many proteins have a hydrophobic core which consists of hydrophobic amino acids, such as alanine, valine, leucine, isoleucine, phenylalanine, and methionine grouped together; often coiled-coil structures form around a central hydrophobic axis.

The energetics of DNA structure assembly were determined by Eric Kool to be mostly caused by the hydrophobic effect, as opposed to Watson-crick base pairing .

The hydrophobic effect can be nullified to a certain extent by lowering the temperature of the solution to near zero degrees; at such temperatures, water prefers to be in an ordered structure and the order generated by hydrophobic patches is no longer as energetically unfavorable. This is neatly demonstrated by the increased solubility of benzene in water at temperatures lower than room temperature.