Objectives The purpose of this study was to evaluate the antimicrobial resistance and frequency of MDR strains in E. coli isolated from patients in two hospitals of Iran. In this descriptive-analytical study, 13322 clinical specimens were collected from two teaching hospitals. The E. coli isolates were identified using standard bacteriological methods. Then, the resistance patterns of the isolates were analyzed by disk agar diffusion method according to the CLSI.Results Out of 13322 clinical samples, 964 (7.23%) isolates of E. coli were identified. In both hospitals, high resistance to ampicillin and cefalexin was presented in 621 (64.4%) and 402 (41.7%) isolates, respectively. The highest antibiotic resistance was observed in burn unit, burn ICU and burn restoration section, while all 8 strains which were isolated from the neonatal-ICU, were sensitive to all tested antibiotics except cefalexin, nitrofurantoin, nalidixic acid, and ampicillin. Also, the bacteria isolated from urine, wound, stool, and blood samples were resistant to all tested antibiotics. Increased resistance to different antibiotics in burn hospital has created increasing concern. Very high resistance to some antibiotics indicates that these drugs are misused in therapeutic centers and highlights that infection control measures should be arranged in the ICUs of our hospitals.