We consider the problem of characterizing the class of those permutation groups that are the symmetry groups of Boolean functions. These are exactly the automorphism groups of hypergraphs. They are also called the relation groups. In this paper we describe those of them that are simple as abstract groups. This is done by combining results based on the classification of finite simple groups with the description of intransitive actions of simple groups. We also obtain a complete characterization of those simple permutation groups that have regular sets, and prove that (with one exception) if a simple permutation group G is a relation group, then every subgroup of G is a relation group.