Fanconi anaemia (FA) is an autosomal recessive disease characterised by progressive pancytopenia, chromosome instability and an increased risk of cancer. The Fanconi Anaemia Complementation Group C (FACC) gene is mutated in patients of complementation group C. Several different forms of FACC mRNA that share the same coding region have been isolated. At least two species result from the use of alternative exons at the 5' end and three result from the use of distinct polyadenylation signals. As a first step toward the characterization of this gene we have isolated the genomic clones corresponding to the 5' region, including a putative promoter and two alternate 5' exons. These exons, named -1 and -1a, were found to be separated by a small intron, with exon -1 located 5' to exon -1a. Further, these exons are flanked by consensus sequences of donor sites at the 5' ends of introns. An acceptor splice site was not evident 5' of exon -1a, suggesting that exon -1 is not spliced onto exon -1a. The sequences upstream of exons -1 and -1a have no obvious TATA or CAAT boxes but include CG-rich sequences. Functional analysis of the sequence upstream of the putative transcription start site of both alternative exons indicates that the region upstream exon -1 is sufficient to drive the expression of the luciferase reporter gene in CaCo-2 cells and that the transcriptional regulation of this gene is complex.