This study was conducted to identify and characterize the multi-drug resistant Escherichia coli isolated from urine and faecal samples collected from Ondo state, between December, 2012 and March, 2013. Escherichia coli isolates (n=206) were identified by conventional microbiology culture and were characterized using biochemical test. The E. coli isolates were subjected to eleven (11) most commonly used antimicrobial agents to determine their resistance. From the result, 100%, 100%, 98.1%, 97.1%, 94.7%, 94.7%, 83.5%, and 67.5%, 35.78%, 35.61% and 19.35% of the tested E. coli isolates from urine and faecal samples were found resistant respectively to ceftazidim, cefuroxime, augumentin, trimethoprime, tetracycline, cefixime, gentamicin, chloramphenicol, ciprofloxacin ofloxacin and nitrofurantoin. Multi-drug resistance (MDR) profile indicated that E. coli isolates were resistant to 7 out of 11 antibiotics tested, 6.79% of the E. coli isolates were resistant to all the eleven antibiotics tested while 0.97% were resistant to at least four antibiotics. However, multi-drug resistance index (MDRI) indicated that all isolates were resistant.