Heat stress is one of the most prominent and deleterious environmental threats affecting plant growth and development. Upon high temperatures, plants launch specialized gene expression programs that promote stress protection and survival. These programs involve global and specific changes at the transcriptional and translational levels. However, the coordination of these processes and their specific role in the establishment of the heat stress response is not fully elucidated. We have carried out a genome-wide analysis to monitor the changes in the translation efficiency of individual mRNAs of Arabidopsis thaliana seedlings after the exposure to a heat shock stress. Our results demonstrate that translation exerts a wide but dual regulation of gene expression. For the majority of mRNAs, translation is severely repressed, causing a decreased of 50% in the association of the bulk of mRNAs to polysomes. However, some relevant mRNAs involved in different aspects of homeostasis maintenance follow a differential pattern of translation. Sequence analyses of the differentially translated mRNAs unravels that some features, such as the 5'UTR G+C content and the cDNA length, may take part in the discrimination mechanisms for mRNA polysome loading. Among the differentially translated genes, master regulators of the stress response stand out, highlighting the main role of translation in the early establishment of the physiological response of plants to elevated temperatures.