Abstract In order to assist with the development of more selective and sensitive methods for thyroid hormone analysis the [M–H] − anions of the iodothyronines T4, T3, rT3, (3,5)‐T2 and the non‐iodinated thyronine (T0) have been generated by negative ion electrospray mass spectrometry. Tandem mass spectra of these ions were recorded on a triple‐quadrupole mass spectrometer and show a strong analogy with the fragmentation pathways of the parent compound, tyrosine. All iodothyronines also show significant abundances of the iodide anion in their tandem mass spectra, which represents an attractive target for multiple reaction monitoring (MRM) analysis, given that iodothyronines are the only iodine bearing endogenous molecules. Characteristic fragments are observed at m/z 359.7 and 604.5 for rT3 but are absent in the spectrum of T3, thus differentiating the two positional isomers. The striking difference in the fragmentation patterns of these regioisomeric species is attributed to the increased acidity of the phenol moiety in rT3 compared with T3. Copyright © 2005 John Wiley & Sons, Ltd.