In order to evaluate the observed high rural ozone levels in the eastern Mediterranean area during summertime, vertical profiles of ozone measured in the period 1994–2008 in the framework of the MOZAIC project (Measurement of Ozone and Water Vapor by Airbus in Service Aircraft) over the eastern Mediterranean basin (Cairo, Tel Aviv, Heraklion, Rhodes, Antalya) were analyzed, focusing in the lower troposphere (1.5–5 km). At first, vertical profiles collected during extreme days with very high or very low tropospheric ozone mixing ratios have been examined together with the corresponding back-trajectories. Also, the average profiles of ozone, relative humidity, carbon monoxide, temperature gradient and wind speed corresponding to the 7% highest and the 7% lowest ozone mixing ratios for the 1500–5000 m height layer for Cairo and Tel Aviv have been examined and the corresponding composite maps of geopotential heights at 850 hPa have been plotted. Based on the above analysis, it turns out that the lower-tropospheric ozone variability over the eastern Mediterranean area is controlled mainly by the synoptic meteorological conditions, combined with local topographical and meteorological features. In particular, the highest ozone concentrations in the lower troposphere and subsequently in the boundary layer are associated with large-scale subsidence of ozone-rich air masses from the upper troposphere under anticyclonic conditions while the lowest ozone concentrations are associated with low pressure conditions inducing uplifting of boundary-layer air, poor in ozone and rich in relative humidity, to the lower troposphere.