This work describes a procedure for the generation of site specific mutations into the chromosome of Streptococcus pneumoniae that does not involve the use of antibiotic resistance marker. A linear fragment of transforming deoxyribonucleic acid (DNA) is constructed by polymerase chain reaction (PCR) (gene splicing by overlap extension) and used to transform competent cells of S. pneumoniae. Selection of transformants is performed by PCR, and typically, 1% of the transformed cells show the expected mutation. By this protocol it is possible to change a single base pair into pnuemococcal genome, as well as obtaining in frame deletions and insertions.