An HLPP workshop was held in conjunction with the 7th HUPO 2008 World Congress in Amsterdam, The Netherlands. The workshop was chaired by Laura Beretta (Fred Hutchinson Cancer Research Center (FHCRC)) and Xiaohong Qian (Beijing Proteome Research Center (BPRC)). The workshop was organized in three sessions: Session 1: The Human Proteome Project: the liver perspective, moderated by John Bergeron (McGill University); Session 2: The comparative analysis of the liver and plasma proteomes, moderated by Young-Ki Paik (Yonsei University) and Session 3: Opportunities for the study of liver diseases within the HLPP, moderated by Chantal Housset (INSERM, France).