This study aimed to evaluate the exposure levels and variation in airborne endotoxin and heavy metals such as aluminum, chromium (Cr), iron (Fe), manganese (Mn), nickel (Ni), zinc, and lead (Pb) in the three different South Korean subway environments (driver room, station office, and underground tunnel) and identify subway characteristics influencing endotoxin and heavy metals levels. Air samples were collected and analyzed using the kinetic Limulus Amebocyte Lysate assay and inductively coupled plasma mass spectrometers. The geometric mean was determined for endotoxin levels (0.693 EU/m3). It was also found that Fe (5.070 µg/m3) had the highest levels in subway environments while Pb (0.008 µg/m3) had the lowest levels. Endotoxin levels were higher in the underground tunnel and lower in the station office; the total heavy metal levels showed the same pattern with endotoxin levels. Endotoxins and total heavy metal levels were higher in the morning than at night. Positive correlations were found between endotoxin and Cr, Fe, Mn, and Ni levels. Given the correlation between airborne endotoxins and heavy metals, further studies with larger sample sizes are needed to identify the correlation between levels of airborne endotoxin and heavy metals.