Airborne in situ measurements of NO, NO2, NOy, CO, CO2, O3, J(NO2), and CN were performed in European thunderstorms during the field experiment EULINOX in July 1998. The measurements in the upper troposphere show enhanced NOx (= NO + NO2) concentrations within thunderstorms and their outflow at horizontal scales from 300 m to several 100 km. The maximum NO mixing ratio measured inside a thundercloud close to lightning (the aircraft was also hit by a small lightning strike) was 25 ppbv. A regional NOx enhancement of 0.5 ppbv over central Europe could be traced back to a thunderstorm event starting ~24 hours earlier over Spain. The fractions of NOx in thunderclouds which are produced by lightning and convectively transported from the polluted boundary layer are determined by using CO2 and CO as tracers for boundary layer air. The analyses show that on average about 70% of the NOx increase measured in the anvil region was found to result from production by lightning and about 30% from NOx in the boundary layer. Thunderstorms are also strong sources of small particles. The peak CN concentrations measured within thunderstorm outflows (>30,000 particles STP cm-3) were distinctly higher than in the polluted boundary layer. The amount of NOx produced per thunderstorm and NO produced per lightning flash was estimated. The results imply that the annual mean NOx budget in the upper troposphere over Europe is dominated by aircraft emissions (0.1 TgN yr-1) in comparison to lightning production (~0.03 TgN yr-1). On the global scale, NOx produced by lightning (mean 3 TgN yr-1) prevails over aircraft-produced NOx (0.6 TgN yr-1).