The quantitative analysis of target substances is an important part of assessing the toxicity of diverse materials. Usually, the quantitation of target compounds is conducted by instrumental analysis such as chromatography and capillary electrophoresis. If solvents are used in the pretreatment step of the target analyte quantification, it would be crucial to examine the solvent effect on the quantitative analysis. Therefore, in this study, we assessed the solvent effects using four different solvents (methanol, hexane, phosphate buffered saline (PBS), and dimethyl sulfoxide (DMSO)) and three toxic compounds (benzene, toluene, and methylisothiazolinone (MIT)). Liquid working standards containing the toxic compounds were prepared by dilution with each solvent and analyzed by gas chromatography-mass spectrometry (GC-MS). As a result, we found that the response factor (RF) values of the target analytes were different, depending on the solvent types. In particular, benzene and toluene exhibited their highest RF values (33,674 ng-1 and 78,604 ng-1, respectively) in hexane, while the RF value of MIT was the highest (9,067 ng-1) in PBS. Considering the correlation (R 2) and relative standard deviation (RSD) values, all target analytes showed fairly good values (R 2 > 0.99 and RSD < 10%) in methanol and DMSO. In contrast, low R 2 (0.0562) and high RSD (10.6%) values of MIT were detected in hexane, while benzene and toluene exhibited relatively low R 2 and high RSD values in PBS (mean R 2 = 0.9892 ± 0.0146 and mean RSD = 13.3 ± 4.1%). Based on these findings, we concluded that the results and reliability of the quantitative analysis change depending on the analyte and solvent types. Therefore, in order to accurately assess the toxicity of target compounds, reliable analytical data should be obtained, preferentially by considering the solvent types.