Salmonella and Shigella are responsible for millions of cases of food-borne illness around the world each year. Until now, the detection of these pathogens still relies on the classical methods of identification such as selective media and serology. Howev-er a novel approaches based on molecular study show great promise for routine clin-ical testing. This study was aimed to investigate the presence Salmonella and Shigel-la isolated from eggs; targeting stn gene in Salmonella and invC gene in Shigella using PCR technique. A total 50 egg samples (domestic eggs) were randomly collect-ed from stores, supermarkets and street vendors around the city. Two Salmonella isolates were found in egg samples 4% (2/50) and one Shigella was found in egg sample 2% (1/50). The Salmonella isolates were positive for the stn gene where as Shigella was positive for the invC gene. The result confirmed that the transfer of these organisms through the food chain poses imminent danger to the consumers and concluded that there is a need for continuous surveillance of eggs especially the locally produced ones, suggested using PCR to minimize the possibility of human infections with Salmonella and Shigella.