Recent studies indicate that the process of liver regeneration involves multiple signaling pathways and a variety of genes, cytokines and growth factors. Protein-protein interactions (PPIs) play a role in nearly all events that take place within the cell and PPI maps should be helpful in further understanding the process of liver regeneration. In this review, we discuss recent progress in understanding the PPIs that occur during liver regeneration especially those in the transforming growth factor beta signaling pathways. We believe the use of large-scale PPI maps for integrating the information already known about the liver regeneration is a useful approach in understanding liver regeneration from the standpoint of systems biology.