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The concentration of polycyclic aromatic hydrocarbons (PAHs) in the atmosphere has been continually monitored since their toxicity became known, whereas nitro-PAHs (NPAHs) and oxy-PAHs (OPAHs), which are derivatives of PAHs by primary emissions or secondary formations in the atmosphere, have gained attention more recently. In this study, a method for the quantification of 18 NPAH and OPAH congeners in the atmosphere based on combined applications of gas chromatography coupled with chemical ionization mass spectrometry is presented. A high sensitivity and selectivity for the quantification of individual NPAH and OPAH congeners without sample preparations from the extract of aerosol samples were achieved using negative chemical ionization (NCI/MS) or positive chemical ionization tandem mass spectrometry (PCI-MS/MS). This analytical method was validated and applied to the aerosol samples collected from three regions in Northeast Asia—namely, Noto, Seoul, and Ulaanbaatar—from 15 December 2020 to 17 January 2021. The ranges of the method detection limits (MDLs) of the NPAHs and OPAHs for the analytical method were from 0.272 to 3.494 pg/m3 and 0.977 to 13.345 pg/m3, respectively. Among the three regions, Ulaanbaatar had the highest total mean concentration of NPAHs and OPAHs at 313.803 ± 176.349 ng/m3. The contribution of individual NPAHs and OPAHs in the total concentration differed according to the regional emission characteristics. As a result of the aerosol samples when the developed method was applied, the concentrations of NPAHs and OPAHs were quantified in the ranges of 0.016~3.659 ng/m3 and 0.002~201.704 ng/m3, respectively. It was concluded that the method could be utilized for the quantification of NPAHs and OPAHs over a wide concentration range.