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Acute gastroenteritis, infectious diarrhea is one of the leading causes of illnesses and death in infants and children throughout the world, especially in developing countries. This is so in Asia, Africa and Latin America, where an estimated 2.5 million deaths occur each year in children less than 5 years of age. The identification and diagnosis in most health laboratories is done only for Salmonella spp. and Shigella spp, through culture, biochemical and serological assays, while Entamoeba histolytica, Giardia intestinalis and helminthes are diagnosed by direct microscopic slide method. The other pathogens, however, are not routinely diagnosed One of the modern techniques for identifying enteropathogens relies on PCR amplification assays with specifically designed nucleotide primers. PCR is suggested, by many investigators to be safer, more sensitive and more rapid than the ordinary culture methods for the diagnosis of bacteria or viruses. Timely diagnosis of Enteropathogen infections in patients with acute diarrhea helps determine appropriate treatment, prevents the unnecessary use of drugs and minimizes the spread of the disease.