We have investigated possible collinearity between the genomes of rice and Arabidopsis by comparing 126 annotated and mapped rice BAC sequences (approximately 20 Mb of sequence) with the annotated and complete Arabidopsis genome (approximately 115 Mb). Although we were able to identify several regions in which gene order is preserved, they are relatively small, and are interrupted by noncollinear genes. Computer simulation showed that these microscale collinearities are above the expectation for a random process. On the other hand, the order of exons within homologous genes (<2.5 kb) was preserved, as expected.