Forkhead-box (FOX) superfamily genes are implicated in carcinogenesis through gene amplification, retroviral integration and chromosomal translocation. FOX superfamily genes within the human genome are classified into 17 or 18 families, designated FOX# (# is alphabet A-Q or R). FOXN1, FOXN2 (HTLF), FOXN3 (CHES1), FOXN4, FOXN5 (FOXR1) and FOXN6 (FOXR2) genes constitute the FOXN gene family. Here, we characterized human FOXN4 gene by using bioinformatics. FOXN4 gene at human chromosome 12q24.12 was found to encode three isoforms. FOXN4 isoform 1 (representative transcript), encoding a 518-aa protein, consists of exons 1-10. FOXN4 isoform 2 (NM_ 213596.1), encoding a 337-aa protein, consists of exons 1, 2, 7v, 8-10. FOXN4 isoform 3, encoding a 314-aa protein, consists of exons 1-5, 7-10. Codon 205-518 of isoform 1 was conserved in isoforms 2 and 3. FOXN4 mRNA was expressed in testis, embryonic stem (ES) cells, uterus tumors, and leiomyosarcoma. FOXN4 was most homologous to FOXN1 among human FOXN family members. FOXN4 and FOXN1 showed 41.3% total-amino-acid identity. FOX domain (codon 192-305 of FOXN4) was well conserved among mammalian FOXN family members. FN14 domain (codon 367-456 of FOXN4) was identified as the novel domain conserved among FOXN4 and FOXN1 orthologs. FOXN4 and FOXN1 orthologs were found to share the common domain structure, consisting of FOX and FN14 domains. This is the first report on comprehensive characterization of the human FOXN4 gene as well as on identification of the FN14 domain.