Apo-1/Fas (CD95) is a transmembrane protein expressed on the cell surface that is involved in apoptosis and plays an important role in the function and regulation of the immune system. Aberrant expression of the Apo-1/Fas gene product has been reported in a number of immune-related disorders, such as autoimmune lymphoproliferative syndrome and systemic lupus erythematosus in humans. Mutations in the coding sequence of the Apo-1/Fas gene have been reported in the former condition, whereas no abnormalities of the gene have been found to account for the increased gene expression noted in SLE. We screened the whole 5' flanking region of the Apo-1/Fas gene encompassing over 2000 bp for mutation(s)/polymorphism(s) using multiplex PCR, single-strand conformation polymorphism (SSCP) analysis and sequencing techniques, and identified two polymorphisms in this region. The first polymorphism is a CG-->CA substitution at -1377 nucleotide position within the silencer region, which neither creates or deletes any restriction enzyme sites but alters the transcription factor SP-1 binding site. This polymorphism is noted in 20% of normal Caucasians. The second polymorphism is an GA-->GG substitution at -670 nucleotide position in the enhancer region that creates a MvaI restriction fragment length polymorphism (RFLP) and abolishes the binding site of nuclear transcription element GAS. The MvaI RFLP is polymorphic with heterozygosity of 52% and the frequency of G and A alleles are 0.49 and 0.51, respectively. The identification and characterisation of these two new polymorphisms, particularly the MvaI RFLP marker, provides new genetic markers and may prove useful for further studies on the regulation of apoptosis mediated by the Apo-1/Fas gene on human chromosome 10q23.