BACKGROUND: Mater is a maternal effect gene required for early embryonic development in mice, and its protein serves as an autoantigen in a mouse model of autoimmune premature ovarian failure. METHODS: Human MATER cDNA was cloned by PCR techniques. The mRNA and protein were determined using hybridization and immunodetection respectively. The cDNA and protein sequences were analysed using bioinformatics software. RESULTS: Human MATER gene spans a ~63 kbp DNA at chromosome 19 and is composed of 15 exons and 14 introns. Expression of its mRNA (~4.2 kb) is restricted to the oocytes. Human MATER cDNA (3885 nt) shows an open reading frame (3600 nt) encoding a polypeptide chain composed of 1200 residues with a predicted molecular mass of 134 236 Da. MATER protein (~134 kDa) was detected in human oocytes. The human and mouse cDNA share 67% homology while their deduced polypeptide chains have 53% identity of amino acids. Also, their protein structures have a number of similar features. CONCLUSIONS: The human MATER and mouse Mater genes and proteins are conserved. Characterization of the human MATER and its protein provides a basis for investigating their clinical implications in autoimmune premature ovarian failure and infertility in women.