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 1.8kb deiodinase type II mRNA in liver, and a truncated (1.3kb) 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 8kb, in liver, and 8kb in kidney, heart, and gill tissues. Expression of the longer (∼8kb) transcript is very low. Real-time PCR confirmed the low expression of transcripts in all tissues, suggested by the Northern blot analysis.