Here we summarize evidence for non-equivalence of two structurally similar active sites in transketolase and other thiamine-dependent enzymes. This non-equivalence takes place when the enzymes interact with various ligands (inhibitors, cations, coenzyme and substrates). Data on different strains in the structure of the holotransketolase subunits are also given. The above results are discussed within the framework of a concept of permanent alternative site oscillation of the transketolase molecule in the presence and in the absence of substrate as a manifestation of a 'flip-flop' mechanism.