This detailed volume presents a set of protocols useful for researchers in the field of recombinant immunoglobulin and alternative scaffold engineering, aptamer development, and generation of molecularly imprinted polymers (MIPs). Part I includes methods that deal with amino-acid based synthetic antibodies. Brief protocols about the generation of antibody libraries are detailed, as well as techniques for antibody selection, characterization, and validation. This section is completed by a brief description of a bioinformatics platform that supports antibody engineering during research and development. Part II contains basic procedures about the selection and characterization of aptamer molecules, and Part III describes fundamental processes of MIP generation and application. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.