Thiamine and its three phosphorylated derivatives (mono-, di- and triphosphate) occur naturally in most cells. Recently, we reported the presence of a fourth thiamine derivative, adenosine thiamine triphosphate (AThTP), produced in E. coli in response to carbon starvation. Here, we show that the chemical synthesis of AThTP leads to another new compound, adenosine thiamine diphosphate (thiaminylated ADP, AThDP), as a side product. The structure of both compounds was confirmed by mass spectrometry and 1H-, 13C- and 31P-NMR and some of their chemical properties were determined. Our results show an upfield shifting of the C-2 proton of the thiazolium ring in adenosine thiamine derivatives compared to the conventional thiamine phosphate derivatives. This modification of the electronic environment of the C-2 proton might be explained by a through-space interaction with the adenosine moiety, suggesting an U-shaped folding of adenosine thiamine derivatives. Such a structure where the C-2 proton is embedded in a closed conformation can be located using molecular modeling as an energy minimum. In E. coli, AThTP may account for 15% of total thiamine under energy stress. It is less abundant in eukaryotic organisms, but is consistently found in mammalian tissues and in some cell lines. Using a HPLC method, we show for the first time that AThDP may also occur in small amounts in E. coli and in vertebrate liver. The discovery of two natural thiamine adenine compounds further highlights the complexity and diversity of thiamine biochemistry, which is not restricted to the cofactor role of thiamine diphosphate.