The effect of elevated CO2 and different levels of nitrogen on the partitioning of nitrogen between photosynthesis and a constitutive nitrogen-based secondary metabolite (the cyanogenic glycoside prunasin) was examined in Eucalyptus cladocalyx. Our hypothesis was that the expected increase in photosynthetic nitrogen-use efficiency of plants grown at elevated CO2 concentrations would lead to an effective reallocation of available nitrogen from photosynthesis to prunasin. Seedlings were grown at two concentrations of CO2 and nitrogen, and the proportion of leaf nitrogen allocated to photosynthesis, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), protein and prunasin compared. Up to 20% of leaf nitrogen was allocated to the cyanogenic glycoside, although this proportion varied with leaf age, position and growth conditions. Leaf prunasin concentration was strongly affected by nitrogen supply, but did not increase, on a dry weight basis, in the leaves from the elevated CO2 treatments. However, the proportion of nitrogen allocated to prunasin increased significantly, in spite of a decreasing pool of leaf nitrogen, in the plants grown at elevated concentrations of CO2. There was less protein in leaves of plants grown at elevated CO2 in both nitrogen treatments, while the concentration of active sites of Rubisco only decreased in plants from the low-nitrogen treatment. These changes in leaf chemistry may have significant implications in terms of the palatability of foliage and defence against herbivores.