Till now, three major spectroscopic techniques, fourier transform infrared (FT-IR), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, have been used for determination of thiol-thione tautomeric forms. Therefore, a novel analytical concept of discrimination of 1,2,4-triazole-3-thione and 3-thiol tautomers using two high-resolution mass spectrometers has been proposed. It comprises the high-performance liquid chromatography (HPLC) hyphenated with electrospray ionization (ESI)-time-of-flight mass spectrometry (ESI-TOF-MS, positive ion mode) followed by in-source collision-induced dissociation (CID) and low-energy CID-tandem mass spectrometry (MS/MS) analysis measured with a Quadruple-TOF-MS instrument. The HPLC column was a Zorbax Stable Bond RP-18 and a rapid isocratic elution. Selected 3-thione and 3-thiol tautomers were rapidly separated, within 6 min and detected both by in-source CID ESI(+)-TOF-MS and CID ESI(+)-QTOF-MS with a high mass accuracy and high sensitivity. The method limits of detection were of 2.8–5.6 pg/μl (at S/N 3:1) for ESI-TOF-MS and 0.25–0.55 pg/μl for ESI-QTOF-MS. The tautomeric form could be easily discriminated by both methods and by the different gas-phase fragmentation patterns. Differences and similarities between in-source CID MS and CID MS/MS spectra have also been presented. These findings were also supported by recorded FT-IR spectra in solid state. The developed methodology using both the high-resolution MS systems is considerably the most sensitive among the others.