A few rare instances are known in which conformational restriction on polypeptide folding patterns by disulfide cross-links results in topological chirality. We now show that, once the role played by covalently bound cofactors (prosthetic groups) in conjugated proteins is taken into account, topological chirality is in fact more common than previously realized. Iron-sulfur proteins are examples of native proteins in which covalently bound Fe4S4 clusters induce topological chirality even in the absence of disulfide cross-links. Quinoproteins with covalently bound cofactors are now recognized to contain catenated substructures, and thus provide the first example of topological complexity in a native protein. The present study strongly suggests that topological chirality may be of wide occurrence among the diverse classes of conjugated proteins.