Deiodinase type II metabolises the prohormone T4 (thyroxine) into the biologically active hormone T3 (3,5,3'-triiodothyronine), at the cellular level in extrathyroidal target tissues. In juvenile lungfish, Neoceratodus forsteri, a typical deiodinase type II is present in most tissues. We have identified the full length of a 1.8 kb deiodinase type II mRNA in liver, and a truncated (1.3 kb) version in brain. Both mRNAs have two in frame UGA codons, but only the liver form has a predicted SECIS structure (form 1) in its 3'-UTR. We also report the presence of additional different length transcripts of deiodinase II mRNA, i.e., 3, 4, and 8 kb, in liver, and 8 kb in kidney, heart, and gill tissues. Expression of the longer (approximately 8 kb) transcript is very low. Real-time PCR confirmed the low expression of transcripts in all tissues, suggested by the Northern blot analysis.