In this work two monoiodothyronines, 3-T1 and 3′-T1, have been analyzed using electrospray ionization tandem mass spectrometry (ESI-MS/MS). Fragmentation patterns were proposed based on our data obtained by ESI-MS/MS. MS2 spectra in either negative or positive ion mode can be used to differentiate 3-T1 and 3′-T1. Based on the relative abundance of fragment ions in MS2 spectra in the negative ion mode, quantification of the 3-T1 and 3′-T1 isomers in mixtures is achieved without prior separation. Solid-phase extraction in combination with ESI-MS/MS provides a practicable procedure that can be used to determine the molar ratio of 3-T1 and 3′-T1 in human serum with an error less than 3%. The detection limits for 3-T1 and 3′-T1 were 0.5 and 0.7 pg/µL, respectively. Copyright © 2006 John Wiley & Sons, Ltd.