Populus trichocarpa is a biological model and a candidate species for bioethanol production. Although intraspecific variation is recognized, knowledge about genetic variation underlying the properties of its lignocellulosic biomass is still incomplete. Genetic variation is fundamental for continuing genetic improvement. In this study, we carried out a comprehensive phenotypic characterization of this species, analyzing a suite of quantitative traits associated with growth performance and wood quality. Traits involved growth rate (height, diameter), phenology (bud flush), and ecophysiology (leaf carbon and nitrogen content and isotopic composition), along with the chemical composition (contents of sugars and lignin) and metabolome of wood. We utilized 460 clones, representing 101 provenances collected from Oregon and Washington. These genotypes were planted in California, in 2009, and sampled after three growing seasons. Trait characterization was carried out by direct measurements, determination of stable isotopes (leaf samples), and technologies based on mass spectrometry (wood samples). A significant clonal effect was observed for most of the traits, explaining up to 76.4 % of total variation. Estimates of “broad-sense heritability” were moderate to high, reaching 0.96 (for date of bud flush). Phenotypic and genetic correlations varied extensively depending on specific traits. In addition, metabolomic analyses quantified 632 metabolites. Twenty-eight of these varied significantly with experimental factors, showing low to moderate heritability and correlation estimates. The results support the presence of significant clonal variation and inheritance for the assessed traits, required for response to genetic selection.