We have isolated and characterised genomic clones spanning the mouse peroxisome proliferator activated receptor alpha gene (PPAR alpha). The gene contains eight exons spanning at least 30 kilobases. The DNA binding domain of PPARa consists of two exons, each encoding one of the zinc fingers. Three exons encode the ligand binding domain and 3' untranslated regions of PPAR alpha. There are two 5' untranslated exons and one exon encoding the N-terminal domain. The 5' flanking region is GC rich and contains several putative SP1 binding sites. The structure of the PPAR alpha gene is unique but shares similar features with related members of the nuclear hormone receptor family.