Field-growing silver birch (Betula pendula Roth) clones (clone 4 and 80) were exposed to elevated CO2 and O3 in open-top chambers for three consecutive growing seasons (1999–2001). At the beginning of the OTC experiment, all trees were 7 years old. We studied the single and interaction effects of CO2 and O3 on silver birch below-ground carbon pools (i.e. effects on fine roots and mycorrhizas, soil microbial communities and sporocarp production) and also assessed whether there are any clonal differences in these below-ground CO2 and O3 responses. The total mycorrhizal infection level of both clones was stimulated by elevated CO2 alone and elevated O3 alone, but not when elevated CO2 was used in fumigation in combination with elevated O3. In both clones, elevated CO2 affected negatively light brown/orange mycorrhizas, while its effect on other mycorrhizal morphotypes was negligible. Elevated O3, instead, clearly decreased the proportions of black and liver-brown mycorrhizas and increased that of light brown/orange mycorrhizas. Elevated O3 had a tendency to decrease standing fine root mass and sporocarp production as well, both of these O3 effects mainly manifesting in clone 4 trees. CO2 and O3 treatment effects on soil microbial community composition (PLFA, 2- and 3-OH-FA profiles) were negligible, but quantitative PLFA data showed that in 2001 the PLFA fungi : bacteria-ratio of clone 80 trees was marginally increased because of elevated CO2 treatments. This study shows that O3 effects were most clearly visible at the mycorrhizal root level and that some clonal differences in CO2 and O3 responses were observable in the below-ground carbon pools. In conclusion, the present data suggests that CO2 effects were minor, whereas increasing tropospheric O3 levels can be an important stress factor in northern birch forests, as they might alter mycorrhizal morphotype assemblages, mycorrhizal infection rates and sporocarp production.