PDX1.2 is expressed in the basal part of the globular-stage embryo, and plays critical roles in development, hypocotyl elongation, and stress response. The Arabidopsis thaliana PDX1.2 protein belongs to a small family of three members. While PDX1.1 and PDX1.3 have been extensively described and are well established to function in vitamin B6 biosynthesis, the biological role of PDX1.2 still remains elusive. Here, we show that PDX1.2 is expressed early in embryo development, and that heat shock treatment causes a strong up-regulation of the gene. Using a combined genetic approach of T-DNA insertion lines and expression of artificial micro RNAs, we can show that PDX1.2 is critically required for embryo development, and for normal hypocotyl elongation. Plants with reduced PDX1.2 expression also display reduced primary root growth after heat shock treatments. The work overall provides a set of important new findings that give greater insights into the developmental role of PDX1.2 in plants.