Abstract: The evolution of genes is usually studied and reconstructed at the sequence level, by comparing and aligning their genomic, transcript or protein sequences. However, including the exon-intron structure of genes in the analysis can provide further and useful information, for example to draw reliable phylogenetic relationships left unsolved by traditional sequence-based evolutionary studies, or to shed further light on patterns of intron gain and loss. So, in this work we present the Perl program designed to retrieve, compare and search for the exon-intron structure in CDS..join features of existing gene annotations. By this means, we can construct an Exon-Intron database (EID), including the phase of intron, the number/size of exon and intron, the pattern of splicing site and the information of alternative splicing (AS).