We report the first comprehensive analysis of the effects of elevated [CO₂] on gene expression in source leaf and stem sink tissues in woody plants. We have taken advantage of coppiced Populus deltoides (Bartr.) stands grown for 3 years under three different and constant elevated [CO₂] in the agriforest mesocosms of Biosphere 2. Leaf area per tree was doubled by elevated [CO₂] but although growth at 800 v. 400 µmol mol^–1 CO₂ resulted in a significant increase in stem biomass, growth was not stimulated at 1200 µmol mol^–1 CO₂. Growth under elevated [CO₂] also resulted in significant increases in stem wood density. Analysis of expression data for the 13 490 clones present on POP1 microarrays revealed 95 and 277 [CO₂]-responsive clones in leaves and stems respectively, with the response being stronger at 1200 µmol mol^–1. When these [CO₂]-responsive genes were assigned to functional categories, metabolism-related genes were the most responsive to elevated [CO₂]. However within this category, expression of genes relating to bioenergetic processes was unchanged in leaves whereas the expression of genes for storage proteins and of those involved in control of wall expansion was enhanced. In contrast to leaves, the genes up-regulated in stems under elevated [CO₂] were primarily enzymes responsible for lignin formation and polymerisation or ethylene response factors, also known to induce lignin biosynthesis. Concomitant with this enhancement of lignin biosynthesis in stems, there was a pronounced repression of genes related to cell wall formation and cell growth. These changes in gene expression have clear consequences for long-term carbon sequestration, reducing the carbon-fertilisation effect, and the potential for increased lignification may negatively impact on future wood quality for timber and paper production.