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Intracellular bacterial pathogens remain a major cause of infection leading to human diseases and death worldwide. With the advent of proteomic technologies, a number of proteomic studies of intracellular bacteria have been carried out to gain insight into the adaptation, survival, or proliferation of bacteria inside host cells. Over 20 intracellular bacterial species have been investigated in various host cells. In this review, we summarize the intracellular bacteria studied by mass spectrometry- or immunostaining-based proteomic techniques, the number of proteins identified for the intracellular bacteria, and the implications of the results in the interaction between the bacteria and their hosts. We also discuss the factors that limit the depth of current proteomic studies of intracellular bacteria and the possible approaches to overcome the limitations.