Comparative genomics utilizes genomic information to estimate structural and functional similarity among living organisms at a given level of organization.  Comparative genomics research can contribute to the: i) comparison of the organization of related genomes to infer the basic processes of genome evolution, ii) transfer of information from model species to related organisms, and iii) integration of information on gene location and expression across species.  Such information can facilitate the assembly of physical maps, development of molecular markers, candidate gene identification, and interspecies gene cloning.  Recent reports have revealed that structural and functional relationships among grass species are complex and that grass genomes are evolving more rapidly than previously thought, thus complicating cross-species comparisons at the DNA sequence level.  As more genomic sequence becomes available, higher resolution maps are possible, cryptic genome duplication events are more easily detected, and better estimates of the rate of evolution of coding and non-coding sequences are possible.  Comparisons of sequence divergence within and among related species may provide an entry point to identification of conserved, non-coding regions that may function in gene expression.  High resolution sequence-based comparative maps will facilitate the use of rice for locating genes of interest in non-model species; however, most applications will require extensive cross-species mapping, sequencing, and analysis at the BAC level.