The spread of tuberculosis often remains undetected and development of disease may occur years after the primary infection. However, tracing chains of transmission is an important task for prevention of new cases, especially for multi-drug-resistant tuberculosis. Today, molecular typing methods have become an important tool for identification and confirmation of epidemiological links between tuberculosis patients in an outbreak situation. Differentiation between strains of Mycobacterium tuberculosis also allows to decide between reactivation because of treatment failure and superinfection. A growing number of typing methods have been developed that differ mainly in their reproducibility and the ability to differentiate between isolates closely related at the molecular level. Based on further standardisation and automation, molecular typing techniques can provide pertinent information for tuberculosis control.