In the framework of the MOZAIC–IAGOS programme, vertical profiles of ozone (O 3 ) and carbon monoxide (CO) have been available since 1994 and 2002, respectively. This study investigates the variability and trend of both species in three tropospheric layers above the German airports Frankfurt and Munich. About 21 300 flights have taken place over the period 1994–2012, which represents the worldwide densest vertical in situ data set of O 3 and CO (with ∼ 96 flights per month on average). The mean vertical profile of ozone shows a strong gradient in the first kilometre during the whole year and in the tropopause region in spring and summer. The mean vertical profile of CO is characterised by high mixing ratios at the ground, a strong decrease in the first kilometre, in particular in winter and autumn, and a moderate one in the free troposphere. O 3 minimises in November–December and shows a broad spring/summer maximum in the lower and mid-troposphere and a sharp maximum in summer in the upper troposphere. The seasonal variation of CO shows a broad minimum in July–October close to the surface and in September–October it occurs higher in the troposphere, while the maximum occurs in February–April in the whole troposphere. Over the period 1994–2012, O 3 has changed insignificantly (at a 95 % confidence level), except in winter where a slightly significant increase (from +0.83 [+0.13;+1.67] % yr −1 in the LT to +0.62 [+0.02;+1.22] % yr −1 in the UT, relative to the reference year 2000) is found. The O 3 5th percentile shows similar upward trends at the annual scale in all three tropospheric layers. All trends remain insignificant for the O 3 95th percentile. In contrast, for CO the mean as well as its 5th and 95th percentiles decrease both at the annual scale and at the seasonal scale in winter, spring and summer (although not always in all three tropospheric layers) with trends ranging between −1.22 [−2.27;−0.47] and −2.63 [−4.54;−1.42] % yr −1 , relative to the reference year 2004. However, all CO trends remain insignificant in autumn. The phase of the seasonal variation of O 3 was found to change in the troposphere. The O 3 maxima moves forward in time at a rate of −17.8 ± 11.5 days decade −1 in the lower troposphere, in general agreement with previous studies. Interestingly, this seasonal shift is shown to persist in the mid-troposphere (−7.8 ± 4.2 days decade −1 ) but turns insignificant in the upper troposphere.