Toxoplasmosis is an important parasitic infection of man and animals. It is well-known that the progression and severity of disease depend on the immunological status of the host, but recent studies suggest that the genetics of the parasite can also play a role. Diagnosis based on clinical appearance and serology is not always easy. However, molecular methods do not depend on an immune response, and allow direct detection of the parasite in biological samples. Thus they can be used to establish a diagnosis when serological tests are not definitive. Multicopy sequences specific for Toxoplasma gondii, e.g., the B1 gene or the 529-bp sequence, are especially useful in molecular tests. Real-time PCR is very sensitive and is a promising technique that is capable of providing a quantitative result. Molecular methods are also used for genotypic characterisation of T. gondii isolates. Analysis of polymorphic sequences determines the precise strain. The choice of sequence is critical when undertaking studies on the correlation between clinical signs and symptoms of disease and the T. gondii genotype. Further studies involving direct genotyping of T. gondii from clinical samples are needed.