The mouse NQO2 cDNA and gene with flanking regions were cloned and sequenced. Analysis of the primary structure of the mouse NQO2 protein revealed the presence of glycosylation, myristylation, protein kinase C and caseine kinase II phosphorylation sites. These sites are conserved in the human NQO2 protein. The mouse NQO2 gene promoter contains several important cis-elements, including the antioxidant response element (ARE), the xenobiotic response element (XRE), and an Sp1 binding site. Northern analysis of eight mouse tissues indicated wide variations in the expression of the NQO2 and NQO1 genes. NQO2 gene expression was higher in liver and testis compared with the NQO1 gene, which was highest in the heart. NQO1 gene expression was undetectable in the testis. Mouse kidney showed significantly higher expression levels of NQO1 compared with NQO2. Brain, spleen, lung, and skeletal muscle showed undetectable levels of NQO2 and NQO1 gene expression. NQO2 activity followed a more or less similar pattern of tissue-specific expression as NQO2 RNA. Interestingly, the NQO2 activity remained unchanged in the NQO1-/-mice tissues compared with NQO1+/+ mice, with the exception of the liver. The livers from NQO1-/-mice showed a 45% increase in NQO2 activity compared with the NQO1+/+ mice. The mouse NQO2 cDNA was subcloned into the pMT2 eukaryotic expression vector which, upon transfection in monkey kidney COS1 cells, produced a significant increase in NQO2 activity. Deletion of 54 amino acids from the N-terminus of the mouse NQO2 protein resulted in the loss of NQO2 expression and activity in transfected COS1 cells. This indicates that deletion of exon(s) encoding the N-terminus of NQO2 from the endogenous gene in mouse embryonic (ES) stem cells should result in NQO2-null mice.