Abstract: Molecular characterization of bacteria associated with diarrhoea in children (0-5) years attending selected hospitals in Makurdi was carried out. A total of 377 stool samples were collected from children attending Federal Medical Centre, General Hospital North Bank and Bishop Murray Memorial Hospital, High level Makurdi. Standard methods involving microbiological, biochemical and molecular analysis using PCR were employed in characterizing bacteria associated with diarrhoea in children (0-5)