To assess the genetic and environmental components of gene-expression variation among trees we used RNA-seq technology and Eucalyptus urophylla x grandis hybrid clones tested in field conditions. Leaf and xylem transcriptomes of three 20 month old clones differing in terms of growth, repeated in two blocks, were investigated. Transcriptomes were very similar between ramets. The number of expressed genes was significantly (P<0.05) higher in leaf (25,665 +/- 634) than in xylem (23,637 +/- 1,241). A pairwise clone comparisons approach showed that 4.5 to 14 % of the genes were differentially expressed (false discovery rate [FDR]<0.05) in leaf and 7.1 to 16 % in xylem. An assessment of among clone variance components revealed significant results in leaf and xylem in 3431 (248) genes (at FDR<0.2) and 160 (3) (at FDR<0.05), respectively. These two complementary approaches displayed correlated results. A focus on the phenylpropanoid, cellulose and xylan pathways revealed a large majority of low expressed genes and a few highly expressed ones, with RPKM values ranging from nearly 0 to 600 in leaf and 10,000 in xylem. Out of the 115 genes of these pathways, 45 showed differential expression for at least one pair of genotype, five of which displaying also clone variance components. These preliminary results are promising in evaluating whether gene expression can serve as possible'intermediate phenotypes' that could improve the accuracy of selection of grossly observable traits.