Satellite-based retrievals of tropospheric NO2 columns are widely used to infer NOx (≡ NO + NO2) emissions. These retrievals rely on model information for the vertical distribution of NO2. The free tropospheric background above 2 km is particularly important because the sensitivity of the retrievals increases with altitude. Free tropospheric NOx also has a strong effect on tropospheric OH and ozone concentrations. Here we use observations from three aircraft campaigns (SEAC4RS, DC3, and ATom) and four atmospheric chemistry models (GEOS-Chem, GMI, TM5, and CAMS) to evaluate the model capabilities for simulating NOx in the free troposphere and attribute it to sources. NO2 measurements during the Studies of Emissions and Atmospheric Composition, Clouds, and Climate Coupling by Regional Surveys (SEAC4RS) and Deep Convective Clouds and Chemistry (DC3) campaigns over the southeastern U.S. in summer show increasing concentrations in the upper troposphere above 10 km, which are not replicated by the GEOS-Chem, although the model is consistent with the NO measurements. Using concurrent NO, NO2, and ozone observations from a DC3 flight in a thunderstorm outflow, we show that the NO2 measurements in the upper troposphere are biased high, plausibly due to interference from thermally labile NO2 reservoirs such as peroxynitric acid (HNO4) and methyl peroxy nitrate (MPN). We find that NO2 concentrations calculated from the NO measurements and NO–NO2 photochemical steady state (PSS) are more reliable to evaluate the vertical profiles of NO2 in models. GEOS-Chem reproduces the shape of the PSS-inferred NO2 profiles throughout the troposphere for SEAC4RS and DC3 but overestimates NO2 concentrations by about a factor of 2. The model underestimates MPN and alkyl nitrate concentrations, suggesting missing organic NOx chemistry. On the other hand, the standard GEOS-Chem model underestimates NO observations from the Atmospheric Tomography Mission (ATom) campaigns over the Pacific and Atlantic oceans, indicating a missing NOx source over the oceans. We find that we can account for this missing source by including in the model the photolysis of particulate nitrate on sea salt aerosols at rates inferred from laboratory studies and field observations of nitrous acid (HONO) over the Atlantic. The median PSS-inferred tropospheric NO2 column density for the ATom campaign is 1.7 ± 0.44 × 1014 molec. cm−2, and the NO2 column density simulated by the four models is in the range of 1.4–2.4 × 1014 molec. cm−2, implying that the uncertainty from using modeled NO2 tropospheric columns over clean areas in the retrievals for stratosphere–troposphere separation is about 1 × 1014 molec. cm−2. We find from GEOS-Chem that lightning is the main primary NOx source in the free troposphere over the tropics and southern midlatitudes, but aircraft emissions dominate at northern midlatitudes in winter and in summer over the oceans. Particulate nitrate photolysis increases ozone concentrations by up to 5 ppbv (parts per billion by volume) in the free troposphere in the northern extratropics in the model, which would largely correct the low model bias relative to ozonesonde observations. Global tropospheric OH concentrations increase by 19 %. The contribution of the free tropospheric background to the tropospheric NO2 columns observed by satellites over the contiguous U.S. increases from 25 ± 11 % in winter to 65 ± 9 % in summer, according to the GEOS-Chem vertical profiles. This needs to be accounted for when deriving NOx emissions from satellite NO2 column measurements.