Background: The emergence of colistin-resistant strains is considered a great threat for the children suffering from diarrhea. This study aimed to screen for the presence of mcr-1 in Escherichia coli (E. coli) isolates collected from children with diarrhea and to compare between genotypic and phenotypic methods for detection of colisitin resistant E.coli carrying mcr-1gene. Methods: Isolation of E.coli was done followed by antimicrobial susceptibility test. Kirby-Baur disc diffusion was used to determine antimicrobial susceptibility, whereas broth microdilution (BMD) and the double disc synergy test (DDST) were used to determine colistin resistance. The screening for mcr-1 was used to investigate one probable mechanism of colistin resistance by PCR. Results: All mcr-1 E.coli isolates were resistant to ampicillin, while resistance to ampicillin/sulbactam, cefazolin, cefoxitin, ceftazidime and trimethoprim-sulphamethoxazol was 94.1% (32/34), 94.1% (32/34), 94.1% (32/34), 85.3% (29/34) and 70.6% (24/34) respectively. All mcr-1carrying E. coli strains were sensitive to tobramycin, amikacin and imipenem. Moderate resistance was noticed to piperacillin/ tazobactam(23/34) 67.6%, gentamycin 47.1% (16/34), and ciprofloxacin 44.1% (15/34). Thirty-one (91.2 %) mcr-1 positiveE. coli strains were multidrug resistant (MDR). Forty five out of 95 (47.4%) of E.coli isolates were positive for mcr-1 by DDST and 34 /95 (35.78%) of E. coli isolates were positive for mcr-1 by PCR. Conclusions: This study reported a high prevalence of colistin resistant E. coli harboring mcr-1 gene in young children in Pediatric Hospital of Assiut University. Broth microdilution is more accurate than DDST in detection of colistin resistance.