Extensive trace gas measurement campaigns were performed in 2005 at the Swiss high-altitude station Jungfraujoch, including measurements of ozone (O₃), carbon monoxide (CO), nitrogen oxides (NO_x = NO + NO₂), the sum of reactive nitrogen species (NO_y), peroxyacetylnitrate (PAN), formaldehyde (HCHO), oxygenated volatile organic compounds (OVOCs), volatile hydrocarbons (HCs), methane (CH₄), and nitrous oxide (N₂O). The air masses arriving at Jungfraujoch experience particular transport pathways and therefore are expected to have characteristic chemical signatures. These characteristics are often masked by mixing with European planetary boundary layer air. In order to address the influence of European emissions, a method to retrieve “background concentrations” based on backward trajectories and statistics was developed and applied to the trace gas observations at Jungfraujoch. This procedure is important to determine baseline values for subsequent assessment of surface air quality targets. Cluster analysis of backward trajectories for “background conditions” shows that the influence of long-range transport is discernible in most of the clusters. Air masses tend to have lower background concentrations whenever transport conditions favor a higher amount of photochemical degradation (e.g., low latitude or no recent contact to emissions). The results of this study represent an alternative to aircraft measurements which are typically used to determine free tropospheric background conditions. They are valuable for comparison with numerical simulations and for policy making, and provide additional information about free tropospheric chemistry.