An $\omega$-tree-automatic structure is a relational structure whose domain and relations are accepted by Muller or Rabin tree automata. We investigate in this paper the isomorphism problem for $\omega$-tree-automatic structures. We prove first that the isomorphism relation for $\omega$-tree-automatic boolean algebras (respectively, partial orders, rings, commutative rings, non commutative rings, non commutative groups, nilpotent groups of class n >1) is not determined by the axiomatic system ZFC. Then we prove that the isomorphism problem for $\omega$-tree-automatic boolean algebras (respectively, partial orders, rings, commutative rings, non commutative rings, non commutative groups, nilpotent groups of class n >1) is neither a $\Sigma_2^1$-set nor a $\Pi_2^1$-set.