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Abstract Background and Objective: CTX-M type extended spectrum beta-lactamases is a rapidly expanding group of enzymes encountered with increasing fre‌quency, especially, in Escherichia coli (E. coli). There are a few reports on phylogenetic background of E. coli isolates from clinical sources of under five-year- old children in Iran. The purpose of this study was phylotyping of E. coli isolates having blaCTX-M and blaCTX-M-15 genes from under five-year- old children with diarrhea and urinary tract infection (UTI). Material and Methods: A total of 121 E. coli isolates (75 diarrheas and 46 UTI) were obtained and identified as E. coli based on standard bacteriological tests. DNA was extracted from E. coli isolates by alkaline lysis method. PCR assay was used because of high frequency of blaCTX-M and blaCTX-M-15 genes in the isolates and also determination of phylogenetic group/subgroups by detection of yjaA and chuA genes and fragment TspE4.C2. Results: The isolates belonged to four phylogenetic groups A (48.77%), B1 (14.04%), B2 (11.57%), and D (25.62%). In the diarrheic isolates,17.37% were positive for blaCTX-M and 14.04% of isolates possessed both blaCTX-M and blaCTX-15genes.Out of 46 UTI isolates, 21.73% were positive for blaCTX-M and 15.21% for blaCTX-M and blaCTX-M-15 genes. Conclusion: A rather high prevalence of E. coli isolates with blaCTX-M and blaCTX-M-15 genes was observed in fewer than five-year- old children in Khoramabad city. Phylotyping of isolates possessing blaCTX-M and blaCTX-15genes showed that most of them belonge to A and D phylo-groups. Keywords: Escherichia Coli, Phylogenetic Group, Extended-Spectrum Beta-Lactamase