Thlaspi arvense, a wild species from the Brassicaceae family, was shown to have a higher level of freezing tolerance than either of its close relatives, the model plant Arabidopsis thaliana or the crop Brassica napus (canola). Over 600 clones were sequenced from a subtractive cDNA library generated from cold treated T. arvense tissue, establishing that T. arvense shared significant sequence identity with both A. thaliana and B. napus (90-92%). In light of the strong sequence similarity between T. arvense and A. thaliana and to exploit the available genomics resources for Arabidopsis, the efficacy of using long 70 mer oligonucleotide whole genome Arabidopsis microarrays was tested for T. arvense. Gene expression in T. arvense leaf tissue during the very early stages of cold acclimation (or cold stress) was assayed at three time points and compared to an untreated control. This analysis highlights some of the difficulties and benefits of using cross-species microarray analysis. The data suggested that T. arvense responds in a similar fashion to cold stress as the model plant A. thaliana. However, for a number of genes quantitative differences in the level and timing of expression were identified. One of the most notable differences suggested that sulphur assimilation leading to the increased production of the methyl donor S-adenosyl-methionine was playing a role in the response of T. arvense to cold stress.