Abiotic environmental stresses cause serious economic losses in agriculture. These stresses include temperature extremes, high salinity and drought. We identified several drought stress-related novel/function unknown coding transcripts (transcription factors and functional genes) and non-coding transcripts (small noncoding transcripts such as microRNA and long noncoding transcripts) using the next generation sequencing method from rice (Oryza sativa L.), and have constructed databases of drought stress-related coding and noncoding transcripts. We used novel gene prediction programs for the selections. The expression level of the each gene was analyzed by real-time PCR. The results ended up the selection of 29 transcription factors, 6 microRNAs and 10 long noncoding RNAs. Currently, we are further characterizing these transcripts. We expect that this study could provide functional information of the drought stress-regulated novel genes, and relationships among novel coding and noncoding transcripts.