The interaction of boron (B) and aluminium (Al) was investigated in 5-day-old seedlings of soybean cv. Maple Arrow. Al treatment inhibited root elongation and callose formation in root tips particularly after 4-h Al treatment. After 10 and 24 h, both parameters indicated increasing recovery from Al stress. B deficiency aggravated Al toxicity compared with B sufficiency. B deficiency did lead to an increase in unmethylated pectin in the first 3 mm of the root tip. This increase in potential binding sites is reflected in generally higher Al contents in root tips of B-deficient plants. A fractionated extraction of Al from the root tips showed that citrate-exchangeable and non-exchangeable Al steeply increased up to 4 h, but then decreased after 10- and 24-h Al treatment faster in B-sufficient than in B-deficient plants. This decrease of Al contents can be explained by an Al-enhanced release of citrate from the root tips after 10-h Al treatment. However, the citrate exudation rate was the same (after 10 h) or even lower (after 24 h) in B-sufficient plants and thus cannot explain the faster decrease in Al contents of the root tips compared with the B-deficient plants. We, therefore, propose that under B deficiency, Al is more strongly bound by the pectic network of the cell wall of the root tips, which delays or prevents the recovery from initial Al stress through exudation of citrate, and thus explains the greater Al sensitivity of B-deficient common bean roots.