Human BCL9 gene is over-expressed in some cases of acute lymphoblastic leukemia (ALL) with t(1;14)(q21;q32). Drosophila segment polarity gene legless (lgs), encoding wingless-armadillo (WNT - beta-catenin) signaling molecule, is the homolog of human BCL9. Here, we identified and characterized human BCL9-like (BCL9L) gene as well as mouse Bcl9-like (Bcl9l) gene by using bioinformatics. Uncharacterized DLNB11 cDNA (AB094091.1) was derived from human BCL9L gene. Nucleotide sequence of mouse Bcl9l cDNA was determined in silico by assembling mouse ESTs BF464707, BQ258167, 5'-truncated BC003321 cDNA, and mouse genome clone RP24-308H8 (AC125129.5). Human BCL9L and mouse Bcl9l genes were found to consist of eight exons. Exon-intron structure was well conserved between human BCL9L and mouse Bcl9l genes. Human BCL9L (1499 aa) showed 94.0% and 34.8% total-amino-acid identity with mouse Bcl9l (1494 aa) and human BCL9, respectively. Six domains (B9H1-B9H6) were conserved among mammalian BCL9 family proteins. B9H1 and B9H2 domains, and N-terminal part of B9H3 domain were identical to HD1, HD2, and HD3 domains conserved between human BCL9 and Drosophila lgs. B9H4, B9H5 and B9H6 were novel domains. B9H4 domain was characterized by multiple Ser-Pro repeats. Human BCL9L mRNA was expressed in fetal brain, adult lung, amygdala, eye, prostate, and also in several types of tumors including pancreatic cancer, prostate cancer, head and neck tumor and embryonal tumor. BCL9L gene was located between BLR1 and UPK2 genes within the commonly deleted region of neuroblastoma at human chromosome 11q23.3. This is the first report on human BCL9L and mouse Bcl9l.