In the world of pathogen-host cell interactions, the autophagic pathway has beenrecently described as a component of the innate immune response against intracellularmicroorganisms. Indeed, some bacterial survival mechanisms are hampered when thisprocess is activated. Mycobacterium tuberculosis infection of macrophages, for example,is impaired upon autophagy induction and the bacterial phagosomes are redirected toautophagosomes. On the other hand, pathogens like Coxiella burnetii are benefited bythis cellular response and subvert the autophagy process resulting in a more efficient replication.We study at the molecular level these two different faces of the autophagy processin pathogen life in order to elucidate the intricate routes modulated by the microorganismsas survival strategies.