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The problem of mechanically formalizing and proving metatheoretic properties of programming language calculi, type systems, operational semantics, and related formal systems has received considerable attention recently. However, the dual problem of searching for errors in such formalizations has attracted comparatively little attention. In this article, we present $\alpha$Check, a bounded model-checker for metatheoretic properties of formal systems specified using nominal logic. In contrast to the current state of the art for metatheory verification, our approach is fully automatic, does not require expertise in theorem proving on the part of the user, and produces counterexamples in the case that a flaw is detected. We present two implementations of this technique, one based on negation-as-failure and one based on negation elimination, along with experimental results showing that these techniques are fast enough to be used interactively to debug systems as they are developed.