Terpene, resin acid and total phenolic concentrations in five-year-old Scots pine (Pinus sylvestris L.) seedlings were analysed after exposure to ambient and realistically elevated (2 × ambient) O3 and CO2 concentrations and their combination in open-top chambers during two growing seasons. Under O3 exposure, limonene concentration in needles and isopimaric concentration in stems decreased significantly. As a response to elevated CO2, α-pinene and total phenolic concentrations in needles increased significantly, while bornyl acetate concentration in needles and palustric + levopimaric and neoabietic acid concentrations in stems decreased significantly. Some terpenes and resin acids were found at lower concentrations in the combined O3 and CO2 treatment than in O3 exposure or elevated CO2. A negative chamber effect was found: seedlings growing inside the chambers with ambient air had significantly lower concentrations of some terpenes and resin acids than seedlings growing outside the chambers. There was a lot of between-tree variation in terpene and resin acid concentrations, which is typical of open-pollinated populations. The results of this study suggest that, at least in short-term experiments, Scots pine secondary metabolites are relatively insensitive to climate change factors. Total phenolics in the needles were the most responsive group showing about 25% increase in elevated CO2, and O3 exposure did not mitigate this CO2 effect. Terpenes and resin acids were less responsive, although some individual compounds showed notable responses, e.g. α-pinene in needles, which increased about 50% in response to elevated CO2. As a consequence, although there were only slight effects on total pools of needle secondary metabolites, considerable O3 and CO2 effects on certain individual compounds might have ecological significance via trophic amplification, e.g. in decomposing processes of needle litter.