The availability of the complete genome sequences of Homo sapiens together with those of taxonomically diverse organisms. provides an opportunity to carry out cross-species comparison. Comparisons or protein sequences from different organisms are significant source of information as these could help in answering questions regarding the fraction of proteins that are shared by humans and organisms representing the three domains of life. viz., archaea. bacteria, and eukaryota. In the present study, a comparative analysis of the proteins encoded by intronless genes in humans was undertaken. We identified 1125 human intronless proteins that are solely present in eukaryotic lineage. More than two-thirds of these eukaryotic specific proteins appear to be mammalia specific while a small fraction of proteins are conserved in bilateria and coelomata, indicating that diversification of these proteins occurred after the divergence of the major lineages of the eukaryotic crown group. A large fraction of mammalia specific proteins are enriched in proteins responsible for transport and binding, cell envelope, and housekeeping function particulary translation. Another 228 intronless proteins are observed that do not exhibit homology to any of the proteins in the database. The distribution of human intronless proteins suggests that lineage specific expansion is one of the most important Sources of organizational diversity in crown-group eukaryotes. The presence of these eukaryotic as well as human specific intronless proteins provides the foundation for rapid analysis of some of the basic processes involved in human genome. (C) 2005 Elsevier Inc. All rights reserved.