In this study, NO<sub>2</sub> columns from the US EPA Models-3/CMAQ model simulations carried out using the 2001 ACE-ASIA (Asia Pacific Regional Aerosol Characterization Experiment) emission inventory over East Asia were compared with the GOME-derived NO<sub>2</sub> columns. There were large discrepancies between the CMAQ-predicted and GOME-derived NO<sub>2</sub> columns in the fall and winter seasons. In particular, while the CMAQ-predicted NO<sub>2</sub> columns produced larger values than the GOME-derived NO<sub>2</sub> columns over South Korea for all four seasons, the CMAQ-predicted NO<sub>2</sub> columns produced smaller values than the GOME-derived NO<sub>2</sub> columns over North China for all seasons with the exception of summer (summer anomaly). It is believed that there might be some error in the NO<sub>x</sub> emission estimates as well as uncertainty in the NO<sub>x</sub> chemical loss rates over North China and South Korea. Regarding the latter, this study further focused on the biogenic VOC (BVOC) emissions that were strongly coupled with NO<sub>x</sub> chemistry during summer in East Asia. This study also investigated whether the CMAQ-modeled NO<sub>2</sub>/NO<sub>x</sub> ratios with the possibly overestimated isoprene emissions were higher than those with reduced isoprene emissions. Although changes in both the NO<sub>x</sub> chemical loss rates and NO<sub>2</sub>/NO<sub>x</sub> ratios from CMAQ-modeling with the different isoprene emissions affected the CMAQ-modeled NO<sub>2</sub> levels, the effects were found to be limited, mainly due to the low absolute levels of NO<sub>2</sub> in summer. Seasonal variations of the NO<sub>x</sub> emission fluxes over East Asia were further investigated by a set of sensitivity runs of the CMAQ model. Although the results still exhibited the summer anomaly possibly due to the uncertainties in both NO<sub>x</sub>-related chemistry in the CMAQ model and the GOME measurements, it is believed that consideration of both the seasonal variations in NO<sub>x</sub> emissions and the correct BVOC emissions in East Asia are critical. Overall, it is estimated that the NO<sub>x</sub> emissions are underestimated by ~57.3% in North China and overestimated by ~46.1% in South Korea over an entire year. In order to confirm the uncertainty in NO<sub>x</sub> emissions, the NO<sub>x</sub> emissions over South Korea and China were further investigated using the ACE-ASIA, REAS (Regional Emission inventory in ASia), and CAPSS (Clean Air Policy Support System) emission inventories. The comparison between the CMAQ-calculated and GOME-derived NO<sub>2</sub> columns indicated that both the ACE-ASIA and REAS inventories have some uncertainty in NO<sub>x</sub> emissions over North China and South Korea, which can also lead to some errors in modeling the formation of ozone and secondary aerosols in South Korea and North China.