An in vitro model system of micropropagated shoots of the commercial clone ‘Villafranca’ of Populus alba (L.) was used to investigate polyamine (PA) biosynthesis and accumulation in response to high concentrations of zinc (Zn) and copper (Cu). Based on leaf symptoms, rate of adventitious root formation and ethylene production, 0.5–1 mM Zn was transiently toxic while 2–4 mM Zn concentrations were increasingly toxic. Free and conjugated putrescine and spermidine accumulated in a dose–response manner and proportionally to toxicity. The expression profiles of the PA biosynthetic genes were analysed by reverse transcriptase polymerase chain reaction in plants exposed to Zn. In both leaves and stems, PaADC and PaODC transcript levels were early enhanced by all Zn concentrations, while those of PaSAMDC were not. In adventitious roots, free and conjugated PA levels also rose, although their composition and reciprocal ratios were different from those of leaves and no changes in transcript levels of PA biosynthetic genes were detected. Several Cu concentrations (5–500 μM) were tested in shoots showing severe leaf toxicity, strongly impaired adventitious root formation and high ethylene production. No changes in PA levels were detected until end of culture. The different timing of the PA response to Zn and Cu, despite their rapid uptake and translocation already at 24 h, is discussed in relation to the extent of leaf toxicity.