A research aircraft is utilized to measure turbulent fluxes, boundary layer and mesoscale structure during a multi-discipline, international land-surface/atmosphere interaction experiment conducted in Sweden — NOPEX. This paper describes the airborne missions during the experiment, including the quality assurance program. The successful calibration of the airborne system is illustrated by internal consistency tests and by a tower–aircraft intercomparison. The latter shows a good agreement between simultaneous aircraft and tower measurements, both for mean variables and for turbulence. Together with the traditional aircraft calibration and data quality procedure this provides a base for the analysis of the field measurements.Two different cases are analyzed. Provided here is a description of the mean boundary layer structure while the analysis of the corresponding turbulence data are described in a companion paper. The analysis of the two cases shows significantly different structure. In one case with moderate wind speed, ∼5ms−1, the structure of the underlying surface seems to control the boundary layer circulation, progressively more for scales larger than ∼5km. This influence fades with altitude, mostly due to the larger effective fetch that causes integration over many different types of surfaces. Surface features with smaller scale, as can be observed by surface radiometric temperature or surface albedo, may influence the lowest 100m locally, but this influence rapidly disappears with height. In the second case, with higher wind speed ∼11ms−1, the vertical coherence for intermediate scales <10km drops significantly while the coherence for the largest scales, >20km, increase. In this case, mesoscale and/or synoptic scale advection is more important than local surface fluxes and the internal mesoscale circulation, possibly along-wind roll vortices, dominate the boundary layer structure. Significant entrainment events also occur in this case, bringing dry and warm free atmosphere air all the way down to the surface.