Inteins are self-splicing proteins capable of fusing protein fragments. A potentially powerful use of intein chemistry would be to polymerize networks of protein domains with customized functions. However, in order to attempt such recombinations, the splicing characteristics of each intein to be used must be well understood. In this study we examined the ability of four inteins (Mtu RecA, Ssp DnaB, Ssp DnaE, Pfu RIR-1) to splice in three general contexts: in trans, in permuted cis and in a combination of the two (ternary splicing). We sought to determine the fidelity of splicing, the relative efficiency of cyclization and the viability of ternary splicing as an approach for combinatorial domain shuffling. Trans splicing displayed high fidelity and reasonable yield with all inteins studied. All permuted cis inteins composed of homologous intein fragments formed cyclic products although permuted cis DnaE inteins partitioned to linear products to a greater extent than other inteins. Permuted cis inteins with heterologous intein fragments were incapable of cyclization, but underwent hydrolysis in some combinations. Ternary splicing successfully formed fusion products with several trans and permuted cis intein combinations. In conclusion, protein recombination using ternary splicing is feasible with a wide variety of inteins which broadens the sequence options available for building domain networks. (Supported by NIH grant AI053800.)