We have developed an alignment tool for comparing protein local surfaces (AltPS). This program enables efficient exhaustive searches of the entire protein surfaces, using a feature vector for a surface atom with 6 to 18 elements to describe the geometrical and physicochemical properties in the local environment, without referring sequence or fold homology. AltPS runs on a personal computer with the input of a pair of PDB coordinates and outputs similarity scores between identified similar surfaces, alignments of the surface atoms, and corresponding superposed coordinates, based on cluster analysis of similar surface regions. In this report, we present some results on the application of AltPS to several protein pairs with similar functions to identify similar functional sites. AltPS can be downloaded from http://d-search.atnifty.com/research.html