Neutrophil cytosolic factor 1, p47phox (NCF1) is a component of the leukocyte NADPH oxidase complex mediating the formation of reactive oxygen intermediates (ROI) which play an important role in host defense and autoimmunity. NCF1 is critical for microbicidal activity. The human p47-phox gene has been well characterized and resides on chromosome 7q11. The start of transcription of the mouse gene has been localized to within 12 nucleotides of the translation start site, similar to the human ortholog. The NCF1 gene colocalizes with two pseudogenes (NCF1B and NCF1C). These two pseudogenes have a GT deletion in exon 2, resulting in a frameshift and an early stop codon. An individual genomic pattern of ncf1 and its two types of pseudogenes (reflected by the DeltaGT/GTGT ratio) may influence the individual capacity to produce ROI, but only marginally influence susceptibility to and outcome of malaria and MS.