Signal peptide peptidase (SPP) is an aspartic proteinase that hydrolyses its substrate within the plane of the cellular membrane. In vertebrates, it plays crucial roles in life processes such as differentiation, embryogenesis, cell signaling and immunological response. We first found SPP in plants. An ortholog of human SPP (AtSPP), and its five AtSPP homologs (AtSPPL1-AtSPPL5), were searched for in the Arabidopsis database. These clones were grouped into three different clusters: AtSPP was grouped with human SPP (HsSPP) orthologs, AtSPPL1 with the HsSPPL3 family, and AtSPPL2-AtSPPL5 with the group of SPP-like proteins of plant origin. AtSPP, AtSPPL1 and AtSPPL2 were examined for their expression profiles by in situ hybridization. AtSPP was strongly expressed in both the shoot meristem of germinating seeds and the inflorescence meristem at the reproductive stage. On the other hand, AtSPPL1 and AtSPPL2 were expressed in the shoot meristem of germinating seeds, but at very low levels in the shoot apex at the reproductive stage. The subcellular localization of AtSPP, AtSPPL1 and AtSPPL2 was investigated using green fluorescent protein (GFP) fusion proteins in cultured 'Deep' cells. GFP-AtSPP localized to the endoplasmic reticulum (ER), and GFP-AtSPPL1 and GFP-AtSPPL2 to the endosomes. These results suggest that AtSPP mediates the cleavage of signal peptide in the ER membrane as well as HsSPP does, and also that AtSPPL1 and AtSPPL2 located in the endosomes have distinct roles in cells.