ZFA is a variant of the material set theory ZF which allows for objects, called atoms or urelements, which may be members of sets, but which themselves have no members (and are not the empty set either). There is a version ZFCA (analogous to ZFC) which includes the axiom of choice (AC). ZFA featured in early independence proofs, notably Fraenkel–Mostowski permutation models, for example showing AC is independent of the rest of the axioms of ZFA.
Zermelo?’s original 1908 axiomatisation of set theory included atoms, but they were soon discarded as a foundational approach as they could be modeled inside of atomless set theory.
From a modern, structural foundations point of view, one can build models of ZFA starting from ZFC by taking a topological group , considering the Boolean topos of sets with an action by an open subgroup (where is allowed to vary), and functions which are equivariant for an open subgroup , where and act on and respectively. The construction outlined at pure set can be varied to construct well-founded pure sets using atoms [DR:which I believe they are elements of the transitive -sets.]