Rice tungro is a serious viral disease of rice resulting from infection by two viruses, Rice tungro bacilliformvirus and Rice tungro spherical virus. To gain molecular insights into the global gene expression changes inrice during tungro, a comparative whole genome transcriptome study was performed on healthy and tungroaffectedrice plants using Illumina Hiseq 2500. About 10 GB of sequenced data comprising about 50 millionpaired end reads per sample were then aligned on to the rice genome. Gene expression analysis revealedaround 959 transcripts, related to various cellular pathways concerning stress response and hormonal homeostasisto be differentially expressed. The data was validated through qRT-PCR. Gene ontology and pathwayanalyses revealed enrichment of transcripts and processes similar to the differentially expressed genes categories.In short, the present study is a comprehensive coverage of the differential gene expression landscapeand provides molecular insights into the infection dynamics of the rice-tungro virus system.