Despite the fact that natural transformation was described long ago in Streptococcus pneumoniae, only a limited number of recombination genes have been identified. Two of them have recently been characterized at the molecular level, recA which encodes a protein essential for homologous recombination and mmsA which encodes the homologue of the Escherichia coli RecG protein. After a survey of the available information regarding the function of RecA, RecG, and other proteins such as the mismatch repair proteins HexA and HexB that can affect the outcome of recombinants, the different levels at which horizontal genetic exchange can be controlled are discussed. It is shown that the specific induction of the recA gene which occurs in competent cells is required for full recombination proficiency. Results regarding the ability of the Hex generalized mismatch repair system to prevent recombination between partially divergent sequences during transformation are also summarized. A structural analysis of homeologous recombinants which suggests that formation of mosaic recombinants can occur independently of mismatch repair in a single-step transformation is also reported. Finally, arguments in favor of an evolutionary origin of transformation as a means of genome evolution are discussed and the different types of recombination events observed which could potentially contribute to S. pneumoniae genome evolution are listed.