Directed evolution experiments rely on the cyclical application of mutagenesis, screening and amplifications in a test tube. During the laboratory evolution of biological molecules, recombination has been used to generate novel sequences in a process known as DNA shuffling. DNA shuffling is a recently developed technique that allows accelerated and directed protein evolution for desired properties in vitro, which recombines and evolves genes to rapidly obtain molecules with improved biological activity and fitness. DNA shuffling is generally achieved by DNaseI treatment and by PCR. This has led to the creation of novel proteins for a wide range of applications. The use of improved enzymes for medical, industrial and environmental purposes is prevalent today, and will be expanding. New applications in vaccine development and disease diagnosis are among the key features of DNA shuffling. However, directed evolution currently requires an uncertain, typically large number of labor-intensive and expensive experimental cycles before proteins with improved function are identified. A simplified and low-cost DNA shuffling protocol for random recombination of homologous genes in vitro is described here.