Graft versus Host Disease (GvHD) is the major life threatening complication after allogeneic stem cell transplantation (SCT), which develops in 35-70% of all SCT despite immunosuppressive prophylaxis. Recently the application of proteomic tools, allowing screening for differentially expressed or excreted proteins in body fluids, could allow detecting specific biomarkers and whole saliva is highly attractive for the non-invasive specimen collection. In this aim we collected salivary specimens of 40 consecutives patients (pts) submitted to alloHSCT between December 2008 to March 2011 in our Institution, which were analyzed by High-Performance Liquid Chromatography (HPLC) coupled to ElectroSpray-Ionization Mass Spectrometry (ESI-MS). Different expressions of S100 proteins family (S100A8, S100A9 and S100A7) were observed. Fourteen pts out of 23 with GVHD showed the presence of S100A8, while the protein was detectable in two pts without GVHD and it was absent in the control group (p 0.001). S100A7 was detectable in 11 pts out 23 with GVHD, while it was absent in the other two group (p 0.0001). S100A9-short was detected in 20 pts with GvHD, in 9 pts without GvHD and in 8 healthy volunteers (p 0.01) Further studies are needed in order to clarify the role of these proteins or as a marker of GvHD or as an index of mucosal inflammation.