Thecolonicfloraininfants suffering from protein energy malnutrition was studied. The study included 56 infants with age ranged from 15 days to 12 months. They did not receive any antibiotic for at least one week prior to the study. They were divided into two groups:Group I included 26 patients suffering from PEM and group II included 30 patients suffering from PEM with diarrhea. Stools specimenswerecollectedandculturedboth aerobically and anaerobically on a variety of enrichment, selective and differential media. Theobtainedcolonies were identified morphologically, biochemically and by the use of the API 20E and API 20A Kit. It was found that the prevalence and mean colony counts of strict anaerobic organisms were reduced in the two groups