Autophagy has recently been described as an intrinsic host defense system for recognizing and eliminating intracellular-invading bacterial pathogens. Some cytoplasmic-invading bacteria are trapped through the process of autophagy and are ultimately degraded within autolysosomal compartments. However, others exhibit highly evolved maneuvers for circumventing autophagic recognition and are capable of surviving and replicating within the cytoplasm. In this chapter, we describe bacterial infectious systems using group A Streptococcus, Shigella flexneri, and Listeria monocytogenes as examples of the interplay between bacteria and autophagy; in addition, methods for investigating bacterial activities related to the recognition of bacteria by the autophagic machinery or the escape of bacteria from autophagy are introduced.