Seventeen soybean cultivars were screened to discern differences in aluminum (Al) sensitivity. The Sowon (Al-tolerant) and Poongsan (Al-sensitive) cultivars were selected for further study by simple growth measurement. Aluminum-induced root growth inhibition was significantly higher in the Poongsan cultivar than in the Sowon cultivar, although the differences depended on the Al concentration (0, 25, 50, 75 or 100 μmol L–1) and the amount of exposure (0, 3, 6, 12 or 24 h). Damage occurred preferentially in the root apex. High-sensitivity growth measurements using India ink implicated the central elongation zone located 2–3 mm from the root apex. The Al content was lower 0–5 mm from the root apices in the Sowon cultivar than in the apices of the Poongsan cultivar when exposed to 50 μmol L–1 Al for 12 h. Furthermore, the citric acid exudation rate was more than twofold higher in the Sowon cultivar. Protein production of plasma membrane (PM) H+-ATPase from the root apices (0–5 mm) was upregulated in the presence of Al for 24 h in both cultivars. This activity, however, decreased in both cultivars treated with Al and the Poongsan cultivar was more severely affected. We propose that Al-induced growth inhibition is correlated with changes in PM H+-ATPase activity, which is linked to the exudation of citric acid in the root apex.