Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, a disease, which is still one of the most significant causes of morbidity and mortality in the world. Mtb is able to silently survive for years inside the lung of an immune-competent host. Bacteria may remain in this stage of persistence until a failure in the immune defenses of the host takes place, as in the case of HIV patients, aged individuals or patients under immune-suppressive therapies. Patients with a reactivated infection can transmit the disease to other individuals in the population. It has been estimated that the lungs of one third of the world population are Mtb reservoirs and therefore the development of new strategies to combat the bacteria in the persistence phase prior to reactivation of the infection is imperative. Experiments in the mouse model of infection have shown that persistent Mtb does not divide or divides very slowly but maintains an active although, restricted metabolism and it is tolerant to antibiotic treatment. This state is usually referred as “non-replicating persistence”. However, the mechanisms required for the entrance of Mtb into such a “persistent state” remain to be determined. Toxin-Antitoxin systems (TAs) can control bacterial growth by regulating the synthesis of macromolecules. It has been proposed that the reversible activation of the toxins can cause a transient growth arrest as part of a global cell response to stress, which would be beneficial to bacterial survival by saving energy. Orthologs of the TAs have been identified in the genome of Mtb. We have focused our study on the VapBC family of TAs since we observed the expression of these genes differentially regulated in Mtb during infection of macrophages. We have obtained data indicating that the over-expression of some of the VapBC genes induces growth arrest specifically in mycobacteria. Moreover, we have observed that these systems are required for the survival of Mtb during chronic infection in mice and for the development of antibiotic tolerance in vitro. The study of the role of the Toxin-Antitoxin systems of Mycobacterium tuberculosis may lead to new approaches to find more effective chemotherapy and to achieve a quicker eradication of the bacteria.