Abstract: The aim of present study is to apply the PCR method for detection of stx1 and stx2 genes in E. coli strains isolated from stool samples. Shiga Toxin-producing Escherichia coli (STEC) have emerged as pathogens that can cause food-borne infections and severe and potentially fatal illnesses in humans, such as Haemorrhagic Colitis (HC) and Haemolytic Uraemic Syndrome (HUS). Of the numerous serotypes of E. coli that have been shown to produce stx, E. coli O157:H7 are frequently implicated in human disease. So, due to serious infections associated with STEC in human, early recognition of STEC is critical for effective treatment of patients. In total 130 isolates of E. coli were recovered from patients by using standard identification procedures. The isolates were subjected to PCR technique for investigation of presence stx1 and stx2 genes.Results revealed the presence of stx1 in 20 isolates (35.5%), stx2 in 28 isolates (49.1%) and stx1 and stx2 both in 9 isolates (15.7%). The present study shows the relatively high prevalence of STEC producing stx1 and stx2 in the region of study. The higher detection rate of stx2 represented the important role of this gene in diarrheal diseases.