Plants require magnesium (Mg) to harvest solar energy and to drive photochemistry. This is probably one the most important physiological functions of this metal as the central atom of chlorophyll (Wilkinson et al., 1990; Hörtensteiner, 2009). Signs of Mg deficiency in most plants usually manifest belatedly as a chlorophyll breakdown between the veins and make their appearance first in mature leaves, systematically progressing from these towards the youngest ones (Bennett, 1997; Hermans & Verbruggen, 2008). The knowledge about Mg2+ uptake by roots, transport to shoots and recycling between organs is relatively limited (Gardner, 2003; Karley & White, 2009). The few physiological reports essentially describe an early impairment in sugar partitioning (in Arabidopsis, Hermans & Verbruggen, 2005; bean plants, Fisher & Bremer, 1993; Cakmak et al., 1994a,b; rice, Ding et al., 2006; spinach, Fisher et al., 1998; spruce, Mehne-Jakobs, 1995 and sugar beet, Hermans et al., 2004, 2005). One dramatic effect of Mg starvation is sugar accumulation in source leaves, before any noticeable effect on photosynthetic activity. Sugar accumulation in source leaf tissues, rather than a reduction in the amount of Mg available for chlorophyll biosynthesis, could be at the root of the decrease in chlorophyll content (Hermans et al., 2004; Hermans & Verbruggen, 2005). A later effect of Mg deficiency is a reduction of plant growth and a modification of the root (R) to shoot (S) biomass allocation. However, observations of the effect of Mg shortage on R : S vary according to the plant model studied and the age of the plant. Early studies report a severe decrease in the root biomass of bean plants (Cakmak et al., 1994a,b) and spinach (Fisher & Bremer, 1993). More recent studies report the absence of an effect on the root system of sugar beet (Hermans et al., 2004, 2005), Arabidopsis (Hermans & Verbruggen, 2005) and rice (Ding et al., 2006) grown hydroponically. Carbon allocation to the youngest leaves is more affected than that to the roots in Arabidopsis thaliana, which could explain why Mg deficiency reduces the growth of young leaves more than the growth of roots (Hermans & Verbruggen, 2005; Hermans et al., 2006). In the present study, we further investigated the transcriptomic response to Mg deficiency in roots and leaves of Arabidopsis, before the outbreak of the visual symptoms described.