Boron (B) is an essential element for plant growth whose deficiency causes an alteration in the expression of a wide range of genes involved in several physiological processes. However, our understanding of the signal transduction pathways that trigger the B-deficiency responses in plants is still poor. The aims of this review are (i) to summarize the genes whose transcript levels are affected by B deficiency and (ii) to provide an update on recent findings that could help to understand how the signal(s) triggered by B deficiency is transferred to the nucleus to modulate gene expression. In this contribution we review the effects of B deficiency on the transcript level of genes related to B uptake and translocation, maintenance of cell wall and membrane function, nitrogen assimilation and stress response. In addition, we discuss the possible mediation of calcium, arabinogalactan-proteins and other cis-diol containing compounds in the signaling mechanisms that transfer the signal of B deficiency to nuclei. Finally, we conclude that the advance in the knowledge of the molecular basis of B deficiency response in plants will allow improving the tolerance of crops to B deficiency stress.