Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance duringanaerobiosis in different plant species. This may be due to the fact that a combination of primary effects, changes due to thepresence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses,are measured together and not differentiated from each other. In order to dissect out these responses, the effect of the presenceor absence of oxygen was investigated using three different experimental designs using rice (Oryza sativa) as a model system. Atotal of 110 metabolites and 9,596 transcripts were found to change significantly in response to oxygen availability in at leastone experiment. However, only one-quarter of these showed complementary responses to oxygen in all three experiments,allowing the core response to oxygen availability to be defined. A total of 10 metabolites and 1,136 genes could be defined asaerobic responders (up-regulated in the presence of oxygen and down-regulated in its absence), and 13 metabolites and 730genes could be defined as anaerobic responders (up-regulated in the absence of oxygen and down-regulated in its presence).Defining core sets of transcripts that were sensitive to oxygen provided insights into alterations in metabolism, specificallycarbohydrate and lipid metabolism and the putative regulatory mechanisms that allow rice to grow under anaerobicconditions. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of thedifferent experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions.Combined with the possibility of selective transcript degradation, these transcriptional processes are involved in the coreresponse of rice to anaerobiosis.