Escherichia coli is a part of human intestinal flora and considered the second most common death factor between children younger than five years. Escherichia coli Shiga-like, Heat-labile toxins and multidrug-resistant are important virulence factors. Therefore, the main targets of this work were molecular diagnosis and characterization of toxine genes Shiga-like and Heat-labile and resistance genes of ciprofloxacin and gentamicin on molecular basis for Escherichia coli isolated from children stool sample in Egypt. The gene detection was carried out using two different approaches which were using chromosome and plasmid. Escherichia coli isolates were resistant to 24 antibiotics including four categories based on their functions. For example, ciprofloxacin, gentamicin, novobiocin and vancomycin. All of tested strains showed band near 300 bp that represents of shiga-like toxin (SLT) gene in their genomic DNA. Heat-labile toxin (LT) fragment ~ 200 bp was detected in plasmid of strain 8H and 8G. Moreover, gentamycin resistance fragment (aac C2) was detected in chromosomal DNA of all strains as a single robust fragment of molecular weight ~ 856 bp. In the case of ciprofloxacin-resistance gene a slight amplification was detected in strain 8G as well as 8H at about 1 kb and 800 bp in genomic, while it was absent in plasmids of tested strains.