This review focuses on what is known about the immune transcriptome during metamorphosis of Xenopus laevis and Silurana (Xenopus) tropicalis. This subject is of importance to obtain a global understanding of the physiological changes operating during metamorphosis. In turn, a good knowledge of the physiology of amphibian metamorphosis may contribute to the fight against amphibian decline and help the development of alternative toxicologic assays. By examining what is known on the expression of innate and adaptive immune genes during metamorphosis, it becomes clear that our knowledge of the anatomy of the tadpole "immunome" is fragmentary. Since a wealth of data sits in cDNA sequences, I am making a first attempt to enrich our knowledge on this subject. I exemplify that mining EST data can rapidly provide us with the necessary tools to unravel the cross-talk between thyroid hormone signalling during metamorphosis and larval immune system changes.