Heme oxygenase (HO) is an enzyme responsible for the physiological degradation of heme to produce iron, CO and biliverdin. The released iron is recycled and represents the major source of this metal in heme homeostasis. A putative role as messenger in a signaling pathway is suggested for CO. Biliverdin, together with bilirubin, may function as an antioxidant. Thus far, three isoforms of HO, HO-1, HO-2 and HO-3 have been described. While HO-1 and HO-2 have been extensively investigated, HO-3 is still an elusive and poorly understood isoform. In this study, we examined the structure of the rat HO-3 gene with genomic PCR. However, we failed to isolate the reported HO-3 gene but, instead, found two HO-3-related genes, tentatively named HO-3a and HO-3b, whose sequences differed slightly from each other. Neither gene had any introns and consisted only of exon 2 through 5 of the HO-2 gene, though their sequences were not completely identical with that of HO-2. A stop codon was introduced within the coding regions of these genes due to frame-shift. The nucleotide sequence of their 5'-upstream region largely agreed with long interspersed nuclear element 3. No HO-3-related mRNAs were amplified by RT-PCR, and no HO-3-related proteins were detected in tissues by Western blot analysis. Our results suggested that there are no functional HO-3 genes in rat and that the HO-3a and HO-3b genes are processed pseudogenes derived from HO-2 transcripts.