The Human Liver Proteome Project (HLPP) is the first initiative of the Human Proteome Organisation (HUPO) to target a human organ/tissue and aims at the establishment of a biological atlas of the liver to advance our understanding of liver functions and to provide the tools to develop new diagnostics and therapeutics for liver diseases. The major achievements of HLPP during its pilot phase (2003-2005) were presented during a one-day workshop held on August 27, 2005, immediately prior to the 4th HUPO World Congress in Munich, Germany. These include (i) the participation of a large number of laboratories worldwide and the initiation of international research collaborations; (ii) the establishment of a management infrastructure and (iii) the development of standard operating procedures and the generation and collection of a first set of expression profile data. A summary of the workshop was subsequently presented by Professor Fuchu He, the Chair of this initiative, during the HUPO 4th Annual World Congress.