The mammalian lamina-associated polypeptide 2 (LAP2) gene encodes six isoforms (LAP2alpha, beta, delta, epsilon, gamma, zeta) that are synthesised from alternatively spliced mRNAs. The mammalian LAP2alpha is one of the predominant isoforms and localised in the nucleoplasm whereas LAP2beta, delta, epsilon, and gamma are integral membrane proteins of the inner nuclear membrane. We have analysed the LAP2 gene structure of the zebrafish Danio rerio as an attractive lower vertebrate model organism. The zebrafish LAP2 (ZLAP2) gene without regulatory sequences spans approximately 19 kb of genomic DNA. It contains 15 exons that encode the isoforms ZLAP2beta, gamma, and omega which are localised in the inner nuclear membrane. By radiation hybrid mapping, we have located the gene onto linkage group 4 between EST markers fc01g04 (213.97cR) and fb49f01 (215.69cR). The identification of a chicken genomic clone comprising the complete coding region of the avian LAP2 gene enabled us to compare the LAP2 gene structure amongst vertebrates. In contrast to the mammalian LAP2 gene, the zebrafish and the chicken sequences do not encode for an alpha-isoform. In parallel we searched for an alpha-isoform in birds using polyclonal and monoclonal LAP2 antibodies specific for the common evolutionary conserved aminoterminal domain present in all isoforms. We detected LAP2beta as the predominant isoform but no LAP2alpha in tissues of 10-day-old chicken embryos and cultured chicken fibroblasts thus confirming the genomic analysis. The comparison of each zebrafish and chicken LAP2 exon with the corresponding exons of the human LAP2 gene demonstrates that the degree of identity at the amino acid level is much higher between the human and chicken than between the human and zebrafish sequences. By Blast search with the nucleotide and amino acid sequences of the human LAP2alpha, we did not find any significant homologies in databases of the zebrafish and chicken sequences. Our data suggest that LAP2alpha is a novelty of mammals.