Inhibition of cGMP-specific phosphodiesterase type 5 (PDE5) has been shown to improve penile erection in patients with erectile dysfunction. We have reported previously the cloning of three PDE5 isoforms from human penile tissues. Here we report the cloning of two PDE5 isoforms from rat penile tissues. The similarity between rat and human PDE5A1-specific sequences were 68 and 88% at the nucleotide and amino-acid levels, respectively. Like the bovine and canine PDE5A1 sequences, the rat PDE5A1 sequence lacks the polyglutamine tract that appears to be unique to the human PDE5A1 sequence. The similarity between rat and human PDE5A2-specific sequences were 64 and 100% at the nucleotide and amino-acid levels, respectively. The equivalent of human PDE5A3-specific sequence was identified in the rat PDE5A gene; however, repeated efforts to clone the putative rat PDE5A3 isoform were not successful. Expression of PDE5A1 and A2 mRNA in various tissues was examined by Northern blotting and reverse transcription-polymerase chain reaction. Results from the two experimental procedures were largely in good agreement and indicated that PDE5A1 and A2 mRNA were expressed in a tissue-specific manner with PDE5A2 being the dominant isoform. International Journal of Impotence Research (2003) 15, 129-136. doi:10.1038/sj.ijir.3900983