Alterations in the target enzymes for beta-lactam antibiotics, the penicillin-binding proteins (PBPs), have been recognized as a major resistance mechanism in Streptococcus pneumonlae, Mutations in PBPs that confer a reduced affinity to beta-lactams have been identified in laboratory mutants and clinical isolates, and document an astounding variability of sites involved in this phenotype. Whereas point mutations are selected in the laboratory, clinical isolates display a mosaic structure of the affected PBP genes, the result of interspecies gene transfer and recombination events. Depending on the selective beta-lactam, different combinations of PBP genes and mutations within are involved in conferring resistance, and astoundingly in non-PBP genes as well.