To overcome the challenges presented by predicted climate change, it is important to understand how crops perceive and respond to high temperatures. In this paper, we performed genome-wide transcriptome analysis of rice to identify immediate early genes strongly induced by high temperature. We compared the effects of high temperature ($37^{circ}C$) treatments (for 0.5 or 1h) of seedlings relative to untreated controls ($28^{circ}C$) using the NSF45K array. We then identified 710 genes exhibiting at least 2-fold up-regulation at both time points. From the comparison of this dataset with other publicly available rice datasets under heat stress [i.e., for 10 and 30 min (early heat response), and 10 h at $42^{circ}C$ (late heat response)], we identified 244 genes and 238 genes at least 2 fold upregulated during the early and late heat responses, respectively. We defined 244 genes as early heat stress responsive group and 238 genes as prolonged heat stress responsive group. Gene ontology (GO) enrichment analysis revealed that a chaperone-mediated protein folding cofactor was the most significantly over-represented GO term associated with the prolonged heat response. Processes involved in cellular protein metabolism, protein folding, response to stress, small GTPase mediated signal transduction, and glycolysis are enriched in both early and prolonged heat responses, suggesting a role for these genes in the general heat stress response. Enrichment of processes involved in cell redox homeostasis, intracellular protein transport, electron transport chain, and regulation of transcription (DNA-dependent) were only identified in the early heat response. In addition, we observed that a large portion of the genes relating to the prolonged heat response were also associated with responses to other abiotic stresses such as drought, salt, cold, and submergence. Our data contribute to a better understanding the molecular mechanism of heat stress response in rice.