The reactive gases perfluoroisobutene and carbonyl fluoride are highly toxic and difficult to analyze in air. For this paper, the available sampling and analysis methods involving gas chromatography/mass spectrometry were investigated for their potential to give unambiguous identification and quantification of perfluoroisobutene and carbonyl fluoride, for which no such methods exist. Although high concentrations of perfluoroisobutene could be analyzed directly by manual split injection, sorbent sampling followed by thermal desorption GC/MS allowed lower concentrations to be analyzed. However, a significant degradation of perfluoroisobutene observed after thermal desorption analysis inspired the use of derivatization of perfluoroisobutene with 3,4‐dimercaptotoluene. The use of Tenax TA sorbent tubes spiked with 3,4‐dimercaptotoluene and trimethylamine in a molar ratio of 1:8 proved successful for the quantification of a unique perfluoroisobutene derivative, and the method was validated for atmospheres in the range of 0.13–152 ppb with a relative standard deviation of less than 20% and an accuracy of 90%. Although carbonyl fluoride was less stable than perfluoroisobutene, direct analysis was possible at high concentrations but the response was not linear. The 3,4‐dimercaptotoluene derivatization method developed was also applicable for quantification of carbonyl fluoride atmospheres.