An increasing number of bacteria are known to adopt intracellular lifestyles. The intracellular niche protects them from the host immune system or antibiotic treatment in human or animal hosts, while providing access to essential nutritional resources. Bacteria can actively modulate the molecular and structural architecture of the intracellular environment to make it hospitable, e.g. by secreting proteins into the cells. For some of the secreted proteins, translocation into the host cell nucleus and direct targeting of nuclear processes have been described; hence, they are termed nucleomodulins (NMs). In this study, we performed an in silico approach to predict putative NMs in S. aureus, E. faecium, E. faecalis, K. pneumoniae, A. baumannii and H. pylori. The results reveal the presence of proteins encoding classical nuclear localization sequences (cNLS), conferring the ability to interact with nuclear importins. This set of candidate NMs will require experimental validation to reveal pathogen-host interactions via direct nuclear targeting.