The spread of antibiotic resistance and the development of new vaccines have focused attention on the epidemiology of Streptococcus pneumoniae over recent years. While serotyping and the determination of antibiotic resistance remain primary methods for characterising pneumococci, molecular typing can add greater discrimination and complementary information. Methods based on restriction fragment length polymorphism within total DNA or non-specific polymerase chain reaction provide information representative of the whole genome and can be used to recognise closely related isolates from different sources, whether in the investigation of possible cross infection at the local level or in the investigation of national or international spread of antibiotic resistant strains. Fingerprinting of penicillin binding protein genes adds further information in the analysis of penicillin resistant isolates. The use of a combination of typing methods to analyse both the genome as a whole and specific loci has led to the realisation that pneumococci undergo horizontal gene transfer much more often than most other bacterial species. In particular the spread of penicillin resistance has been characterised by a combination of the spread of epidemic strains, transfer of chromosomal resistance genes from such strains into other genetic backgrounds, and transfer of capsule genes resulting in the switch of serotypes within strains. In the future molecular typing will have an important role in discovering whether widespread vaccination leads to genetic modification of the pneumococcal population causing invasive disease.