The mto1-1 mutant of Arabidopsis thaliana over-accumulates soluble methionine (Met) up to 40-fold higher than that in its Col-0 wild type. In order to identify genes regulated by altered Met concentrations, microarray analysis of gene expression in young rosettes and developing siliques of the mto1-1 mutant were performed. Expression of selected genes was then examined in detail in three developmental stages of the mto1-1 mutant using a combination of Northern hybridisation analysis and real-time PCR. Eight genes were identified that had altered mRNA accumulation levels in the mto1-1 mutant compared to that in wild-type plants. Three of the genes have known roles in plant development unrelated to amino acid biosynthesis. One other gene up-regulated specifically in mto1-1 rosettes shared similarity with the embryo-specific protein 3 (ATS3). Two novel genes, referred to as AtMRD1 and AtMRU1, were also identified that were expressed in a developmental manner in wild-type Col-0 and do not share sequence similarity with genes of known function. AtMRD1 was strongly down-regulated in both rosette and young silique tissues of the mto1-1 mutant. AtMRU1 was up-regulated approximately 3-fold in young mto1-1 rosettes and exhibited a developmental response to the mto1-1 mutation.