When World War II broke out, he enlisted into the US Navy, which assigned him to the University of California's V-12 program.

Vaught then began afresh under the supervision of Alfred Tarski, completing in 1954 a thesis on mathematical logic, titled Topics in the Theory of Arithmetical Classes and Boolean Algebras.

Vaught's "Never 2" theorem states that a complete first-order theory cannot have exactly two nonisomorphic countable models.

He considered his best work his paper "Invariant sets in topology and logic"[citation needed], introducing the Vaught transform.

He is known for the Tarski–Vaught test for elementary substructures, the Feferman–Vaught theorem, the Łoś–Vaught test for completeness and decidability, the Vaught two-cardinal theorem, and his conjecture on the nonfinite axiomatizability of totally categorical theories (this work eventually led to geometric stability theory).