In the present open-top chamber experiment, two silver birch clones (Betula pendula Roth, clone 4 and clone 80) were exposed to elevated levels of carbon dioxide (CO2) and ozone (O3), singly and in combination, and soil CO2 efflux was measured 14 times during three consecutive growing seasons (1999–2001). In the beginning of the experiment, all experimental trees were 7 years old and during the experiment the trees were growing in sandy field soil and fertilized regularly. In general, elevated O3 caused soil CO2 efflux stimulation during most measurement days and this stimulation enhanced towards the end of the experiment. The overall soil respiration response to CO2 was dependent on the genotype, as the soil CO2 efflux below clone 80 trees was enhanced and below clone 4 trees was decreased under elevated CO2 treatments. Like the O3 impact, this clonal difference in soil respiration response to CO2 increased as the experiment progressed. Although the O3 impact did not differ significantly between clones, a significant time × clone × CO2× O3 interaction revealed that the O3-induced stimulation of soil respiration was counteracted by elevated CO2 in clone 4 on most measurement days, whereas in clone 80, the effect of elevated CO2 and O3 in combination was almost constantly additive during the 3-year experiment. Altogether, the root or above-ground biomass results were only partly parallel with the observed soil CO2 efflux responses. In conclusion, our data show that O3 impacts may appear first in the below-ground processes and that relatively long-term O3 exposure had a cumulative effect on soil CO2 efflux. Although the soil respiration response to elevated CO2 depended on the tree genotype as a result of which the O3 stress response might vary considerably within a single tree species under elevated CO2, the present experiment nonetheless indicates that O3 stress is a significant factor affecting the carbon cycling in northern forest ecosystems.