Hypoxically induced tolerance to anoxia in roots of tomato (Solanum lycopersicum) was previously shown to depend on sucrose and the induction of sucrose synthase. In contrast to maize, root hexokinase (HXK) activities did not increase during hypoxia and glucose was unable to sustain glycolytic flux under anoxia. In this paper, we asked whether hypoxic metabolism in roots would be altered in transgenic tomato plants overexpressing either a plant (Arabidopsis) or a yeast (Saccharomyces cerevisiae) HXK and whether such modifications could be related to improved energy metabolism and consequently root tolerance under anoxia. Tomato plants grown hydroponically with shoots always maintained in air were submitted to a 7 d hypoxic treatment applied by stopping air bubbling. A combination of techniques including (1)H-nuclear magnetic resonance spectroscopy, RT-PCR and enzyme analyses was used to obtain a broad picture of hypoxic root metabolism. In normoxic conditions, HXK overexpression resulted in higher ADP and AMP levels only in roots of AtHXK1 transgenic plants. During hypoxic treatment, oxygen levels in the hydroponic tank decreased rapidly to 5 kPa within the first 2 d and then remained at 5 kPa throughout the 7 d experiment. Oxygen levels were similar at 5 and 20 cm below the water surface. A decline of the adenylate energy status was observed after 2 d of hypoxic treatment, with a further decrease by 7 d in roots of non-transgenic (WT) and ScHXK2, but not in AtHXK1 transgenic plants. Sucrose synthase activity increased to comparably higher levels at 7 d of hypoxic treatment in WT and ScHXK2 compared with AtHXK1 roots. Differences between WT and the transgenic plants are discussed with respect to the metabolic response to low (hypoxia) but not zero (anoxia) oxygen.