Phylogenetic profiles have been widely applied in functional genomics research, especially in the prediction of protein-protein interactions (PPIs). A key issue in phylogenetic profiling is how to effectively select reference organisms from the available hundreds of genomes. In this study, we performed an assessment of reference organisin selection based on the genetic distance between the target organism and 167 reference organisms. We found that inclusion of reference organisms front all distance levels had better performance in the prediction of PPIs than that at each distance level. The PPI prediction reached an optimal level when 70% of the reference organisms at all distance levels were selected: and this performance was similar to that in the optimal condition based on the taxonomy tree in our previous study. Because measurement of genetic distance is direct and simple compared to the topology of the taxonomy tree, we suggest selecting reference organisms based on genetic distance in the construction of phylogenetic profiles. (c) 2007 Elsevier Inc. All rights reserved.