Since the widespread expanse of heterologous protein expression enabled by genetic cloning, the inability to produce active recombinant protein has been the main bottleneck in the biotechnology enterprise. Similarly, we have been severely hindered in our ability to obtain high-quality, purified protein in order to perform X-ray crystallography, NMR spectroscopy, or CD spectroscopy for structural biology. In addition, protein folding is an important prerequisite for the production of efficacious protein-based therapeutics and a crucial concern in the design and generation of de novo proteins. Despite such widespread importance, it is not possible to ad hoc identify the sequence determinants of physiochemical structure for a particular amino acid polymer. To overcome these limitations, our research has focused on the exploitation of native cellular processes in bacteria to engineer the folding properties of desired proteins or peptides through laboratory evolution. By extending and exploiting the intrinsic folding quality control capacities of the protein trafficking pathways in Escherichia coli we have developed a suite of genetic assays for isolating folding-enhanced proteins from recombinant libraries. These techniques have been used for: (1) antibody engineering, (2) fluorescent protein evolution, and (3) the isolation of difficult-to-fold recombinant proteins. Our progress suggests that protein engineering coupled with high-throughput approaches to screening or selecting from recombinant libraries should help to alleviate many of the confines associated with de novo protein design, structural biology, and biotechnology.