Molecular techniques have become an important tool in Epstein-Barr virus diagnostics. In recent years novel real-time PCR formats and in situ techniques have been developed that offer increased time efficiency, reduced cross-contamination, high reproducibility, high sensitivity and allow determination of viral loads. In the near future, widespread clinical application of these diagnostic modalities may provide increased knowledge of the pathophysiology of Epstein-Barr virus infection and may optimize treatment or even explore novel Epstein-Barr virus-related diseases. The monitoring of Epstein-Barr virus viral loads in different tissue compartments is currently being effectively used to assess the treatment response or prognosis in patients with oncological diseases or immunosuppression. This may also gain increasing importance in the nononcological environment. However, the general acceptance of molecular techniques will largely depend on improved standardization.