This study used various methods to evaluate duct cleanliness and identify the levels of deposited dust in the HVAC systems of subway stations, as well as identifying the characteristics of the pollution sources at the stations. Levels of deposited dust were determined in two subway stations in Seoul from September 2011 to January 2012. The levels of dust deposited on ducts of the stations were measured by visual inspection, the quantitative vacuum test (VT), and the deposit thickness test (DTT). The VT results confirmed that no subway station exceeded a dust deposit of 1.0 g/㎡, which is the recommended surface contamination limit when using the VT method. However, in some supply ducts, the thickness of the dust layer exceeded 60.0㎛, the recommended surface contamination limit when using the DTT method. The visual inspection indicated that platform pollution in subway station A was higher than in the HVAC and waiting rooms, but the difference was insignificant (p = 0.852). At subway station B, the waiting room had a slightly higher level of deposited dust, but the difference was insignificant (p = 0.438). The inspected areas were divided into HVAC rooms, return lines, and supply lines according to ventilation type. Although all three inspections revealed that return lines had the highest levels of deposited dust, the difference was insignificant. The correlation between the results of the visual inspection and VT methods, and between the results of visual inspection and DTT methods were both significant (p >0.01) with r = 0.815 and 0.818, respectively. It was confirmed that the results of a qualitative visual inspection method corresponded relatively well with the results of the quantitative VT and DTT methods. Analyses of eight heavy metals in the HVAC systems of the subway stations indicated that the inclusion ratios of iron (Fe), zinc (Zn), and magnesium (Mg) were 80.75–93.6%, 2.94–15.64%, and 1.63–1.82%, respectively. Traces of other heavy metals (As, Cd, Cu, Pb, and Cr) were also detected.