Concentrations of carbon monoxide (CO) and nitrogen oxides (NOx) were measured from 14–17 November 2008 in a cross-mountain Hsuehshan traffic tunnel stretching 12.9 km and containing eastward and westward channels. Traffic and pollutant concentrations during the weekends exceeded those during the weekdays. Measured concentrations of CO at the two tunnel outlets (14.45–22.77 ppm) were approximately three times higher than those at the two tunnel inlets (3.17–7.33 ppm), while concentrations of NOx at the two tunnel outlets (1.92–2.88 ppm) were approximately four to five times higher than those at the two tunnel inlets (0.32–0.78 ppm). The outlet of vertical draft 2 had the highest pollutant concentrations (CO = 12.27 ppm; NOx = 1.85 ppm), followed by vertical drafts 1 and 3. The emission factors for the upslope, west-ward lanes (CO = 1.90 ± 0.43 g/km-veh; NOx = 0.38 ± 0.07 g/km-veh) are higher than those for the down-slope, eastward lanes (CO = 1.45 ± 0.13 g/km-veh; NOx = 0.26 ± 0.03 g/km-veh). High traffic volume and low traffic speed result in high concentrations and emission factors of the pollutants in the tunnel.