We report that the positions of minor, U12 introns are conserved in orthologous genes from human and Arabidopsis to an even greater extent than the positions of the major, U2 introns. The U12 introns, especially, conserved ones are concentrated in 5′-portions of plant and animal genes, where the U12 to U2 conversions occurs preferentially in the 3′-portions of genes. These results are compatible with the hypothesis that the high level of conservation of U12 intron positions and their persistence in genomes despite the unidirectional U12 to U2 conversion are explained by the role of the slowly excised U12 introns in down-regulation of gene expression. Reviewers: This article was reviewed by John Logsdon and Manyuan Long. For the full reviews, please go to the Reviewers' Reports section. © 2008 Basu et al; licensee BioMed Central Ltd.