In order to obtain information about the metabolism of methanol in plants, gene expression in response to methanol stimulation was analysed in leaves of Arabidopsis thaliana through the use of a 26,090 element oligonucleotide microarray. Following confirmation of data and the application of selection criteria, a total of 484 (1.9%) transcripts were shown to be regulated in response to a 10% methanol application. Samples were taken at 1, 24 and 72 h. Of the total identified transcripts, only 20 were shared between all three time points of which only two were down-regulated. Based on functional category analysis of these genes, at 1 h, the largest categories were metabolism, cell communication/signal transduction processes, defence genes associated with transcription and aspects of RNA processing; a few related to cell division and growth; but none were associated with photosynthesis. At 24 and 72 h, the number and overall proportion of regulated transcripts associated with metabolism increased further. Direct measurement of anthocyanin and flavonoid content confirmed that methanol-regulated transcripts corresponded to flavonoid pathways. Within the functional class metabolism, genes encoding detoxification proteins represented by far the most strongly regulated group. These included, cytochrome P450's, glucosyl transferases and members of the ABC transporter family. It is concluded that exposure to methanol affects the expression of hundreds of genes and that multiple detoxification and signalling pathways are activated.