mRNA of the putative Arabidopsis flavin mono-oxygenase encoded by At1g19250 (here designated AtFMO GenBank accession no. NM_101783) accumulated to high levels in the acd11 and lsd1 mutants that exhibit run-away cell death, but not in mutants with constitutive defense responses. AtFMO mRNA accumulation occurred at the transcriptional level because a fusion between the AtFMO promoter and the GUS reporter was induced in acd11 compared to wild type. AtFMO::GUS activity also appeared significantly earlier in wild type plants inoculated with avirulent strains of Pseudomonas syringae compared to a virulent strain. In addition, a close barley homolog was identified by differential display and shown also be induced by pathogen infection. AtFMO::GUS was induced by the fungal toxin fumonisin B1 and by superoxide generation, but not by treatments with hydrogen peroxide, ozone or nitric oxide. During normal development, AtFMO::GUS activity increased from very low, basal levels in young leaves to fairly high levels in the senescing regions of old leaves. The correlation between AtFMO expression and occurrence of cell death suggests that AtFMO mRNA and the AtFMO::GUS reporter are amenable markers for certain forms of defense and cell death.