To evaluate two-dimensional gel electrophoresis (2DGE) and mass spectrometry in the studies of the serum proteins expressed in patients with BPH and those with high-grade prostatic intraepithelial neoplasm (HGPIN).We extracted serum proteins from BPH and HGPIN patients by 2DGE and cut the differentially expressed interesting protein spots from the gel. Then we digested the proteins, obtained the peptide mass fingerprint by mass spectrometry and identified the proteins through database retrieval.We successfully achieved the 2DGE maps of the serum proteins from the BPH and HGPIN patients, obtained 1 421-1 532 protein spots from the 2D map of HGPIN and 1 466-1 778 from that of BPH. Based on peptide mass fingerprinting, 9 of the protein spots were identified. Serum amyloid A was found to be expressed in the HGPIN group, but weakly or not at all in the BPH.Proteomics can be applied to the study of the serum proteins in BPH and HGPIN patients. It can afford experimental evidence for the early diagnosis and development HGPIN, promote the search of functional and specific proteins of prostate diseases and shed new light on the network mechanisms of the problems.