This study investigates the transcript regulation in salt-tolerant rice (var Pokkali) in response to high salinity using microarrays. NaCl at 150 mM reduced photosynthesis to one-tenth of the prestress value within minutes. Microarray hybridizations were performed to probe changes in transcripts from 15 minutes to 1 week after salt shock. Approximately 10% of the transcripts in Pokkali were significantly upregulated or downregulated within 1 hour of salt stress. The initial differences between control and stressed plants continued for hours but became less pronounced as the plants adapted over time. The analysis of salinity-sensitive rice (var IR29) showed a delayed initial response and later downregulation of transcription and death. The upregulated functions observed in Pokkali at different time points during stress adaptation changed over time, including increased protein synthesis and turnover, induction of stress-responsive transcripts, and defense-related functions. After 1 week, the nature of upregulated transcripts, such as aquaporins, indicated recovery. The study highlights the importance of early transcript induction in preparing the plant for defensive mechanisms and the role of subtle transcript regulation in maintaining cellular homeostasis under salinity stress.This study investigates the transcript regulation in salt-tolerant rice (var Pokkali) in response to high salinity using microarrays. NaCl at 150 mM reduced photosynthesis to one-tenth of the prestress value within minutes. Microarray hybridizations were performed to probe changes in transcripts from 15 minutes to 1 week after salt shock. Approximately 10% of the transcripts in Pokkali were significantly upregulated or downregulated within 1 hour of salt stress. The initial differences between control and stressed plants continued for hours but became less pronounced as the plants adapted over time. The analysis of salinity-sensitive rice (var IR29) showed a delayed initial response and later downregulation of transcription and death. The upregulated functions observed in Pokkali at different time points during stress adaptation changed over time, including increased protein synthesis and turnover, induction of stress-responsive transcripts, and defense-related functions. After 1 week, the nature of upregulated transcripts, such as aquaporins, indicated recovery. The study highlights the importance of early transcript induction in preparing the plant for defensive mechanisms and the role of subtle transcript regulation in maintaining cellular homeostasis under salinity stress.