When assessing the inhalation toxicity of diverse inhalable substances, a first step is accurate quantitative analysis. In this study, we developed a method for the quantitative analysis of methylisothiazolinone (MIT) and methylchloroisothiazolinone (CMIT), main components in humidifier disinfectants. A simple thermal desorption (TD) method was used to analyze the CMIT/MIT. Using this method, sample loss during aerosolization was minimized compared with other more complicated pretreatment methods, like solvent absorption and extraction (SV). The results of the TD and SV methods were compared to determine the optimal analytical system for CMIT/MIT analysis. In both methods, the concentration of MIT increased systematically with increasing the CMIT/MIT aerosol concentration (R2>0.98). The MIT contents in the aerosol given by the two analytical methods were somewhat similar (MIT content=1.52% (sample solution), 1.43% (TD) and 1.18% (SV)). In contrast, the measured CMIT content in the aerosol was different depending on the type of pretreatment used. The CMIT content was 2.90% for the TD method, while that for the solvent method recorded 0.75% (CMIT content of the sample solution=4.66%). We confirmed that the sample loss of the CMIT with high reactivity occurred in the complicated sampling and pretreatment steps of the SV method.