Burning of fuels from the transport sector is one of the main sources of air pollutants emission in urban areas. In order to implement public policies concerning air quality and public health, there is a need to develop emission inventories. Measurements inside traffic tunnels can provide an evaluation of emission factors of vehicles in-use in real conditions. In this paper, we show measurements of air pollutants for a mixed vehicle fleet, heavy- and light-duty vehicles (HDVs and LDVs), in two tunnels in the metropolitan region of Sao Paulo in 2011 in order to calculate the pollutant emission factors (EFs). Measurements of carbon dioxide, carbon monoxide (CO), nitrogen oxides (NOx) and particle matter (PM2.5) were taken. High concentrations related to high-density traffic, especially during weekdays. EFs were heavily influenced by the pollutant species loads, so the total vehicle traffic and the fraction of HDV. The EF values for HDV were 3.6 and 9.2 g km−1, for CO and NOx, respectively (5.8 and 0.3 g km−1 for LDV). To determine EF estimates, parameters such as velocity of the air, cross-sectional area and length of the tunnel and vehicles passing at 1-h time interval were considered.