Diarrhoea continues to be one of the most common causes of morbidity and mortality among infants and children in developing countries. Diarrhoeagenic Escherichia coli (DEC) is an emerging agent among pathogens that cause diarrhoea. Between March 2011 and January 2012, a total of 600 stool specimens from children younger than 5 years of age (450 with and 150 without diarrhoea) were investigated for enteroaggregative E. coli (EAEC), enterohaemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC) using PCR. Antimicrobial susceptibility testing was performed following Clinical and Laboratory Standards Institute guidelines. The prevalence of DEC pathotypes was 30.4% (137 patients) and 12% (18 patients) in the diarrhoea group and the control group, respectively. The most frequently isolated pathotype in diarrhoeal children was ETEC. This pathotype was detected significantly more often in children with diarrhoea (14.4%) than in children without diarrhoea (5.3%). EAEC and EPEC were detected with slightly higher frequencies in children with (8 and 4.2%, respectively) than in children without (4.6 and 2%, respectively) (P>0.05) diarrhoea. EHEC was only detected in children with diarrhoea (3.8%). Of the children from the diarrhoea group, 10% were colonized with more than one DEC pathotype. The DEC isolates exhibited high-level resistance to erythromycin (100%), azteronam (80.7%), amoxicillin (74.4%) and tetracycline (69.3%), and 86.4% of isolates were multidrug resistant. In conclusion, ETEC continues to be an important agent associated with diarrhoea in children from Tabriz, Iran.