We have cloned and partially characterized the rabbit FMO1 gene as a first approach to understanding mechanisms controlling its tissue-specific expression. The isolated clones contain 14 kb of 5' flanking information and approximately 30 kb of the structural gene, but do not include the 3'-end. Two upstream exons were defined, both encoding 5' leader information. The first exon, termed exon 0, contains information not previously reported. The second exon, termed exon 1, contains information previously reported for the rabbit FMO1 cDNA. Protein coding information begins seven nucleotides from the start of exon 2. A single transcription start site was localized in exon 1, while a cluster of sites were defined in exon 0, consistent with two alternative promoters. Transcripts initiating in exon 0 do not contain exon 1 information due to alternative processing and represent the major FMO1 mRNA. Neither promoter contains a TATA box or GC islands, although the exon 1 promoter does share some sequence identity with initiator-type elements. Homologous sequences to several known transcription factor binding sites were found in the upstream region of the FMO1 promoters. Both promoters were active in directing luciferase expression when transiently transfected into human HepG2 cells, although the data are consistent with both requiring upstream enhancer sequences. Consistent with this observation, DNase I hypersensitive sites were mapped to a 600-bp region immediately upstream of exon 0 using liver nuclei. No such sites were detected with nuclei from lung. Differential DNA methylation also was not observed between these two tissues.