In the framework of the In Service Aircraft for Global Observing System (IAGOS) program, airborne in-situ O3 and CO measurements are performed routinely using in-service aircraft, providing vertical profiles from the surface to about 10–12 km. Due to the specificity of IAGOS measurements (measurements around busy international airports), uncertainties exist on their representativeness in the lower troposphere as they may be impacted by emissions related to airport activities and/or other aircraft. In this study, we thus investigate how the IAGOS measurements in the lower troposphere compare with nearby surface stations (from the local Air Quality monitoring network (AQN)) and more distant regional surface stations (from the Global Atmospheric Watch (GAW) network). The study focuses on Frankfurt but some results at other European airports (Vienna, Paris) are also discussed. Results indicate that the IAGOS observations close to the surface do not appear to be strongly impacted by local emissions related to airport activities. In terms of mixing ratio distribution, seasonal variations and trends, the CO and O3 mixing ratios measured by IAGOS in the first few hundred metres above the surface have similar characteristics to the mixing ratios measured at surrounding urban background stations. Higher in altitude, both the difference with data from the local AQN and the consistency with the GAW regional stations are higher, which indicates a larger representativeness of the IAGOS data. Despite few quantitative differences with Frankfurt, consistent results are obtained in the two other cities Vienna and Paris. Based on 11 years of data (2002–2012), this study thus demonstrates that IAGOS observations in the lowest troposphere can be used as a complement to surface stations to study the air quality in/around the agglomeration, providing important information on the vertical distribution of pollution.