The increase in antimicrobial resistance in developed and developing countries is a global public health challenge. In this context β-lactamase production is a major contributing factor to resistance globally. The aim of this study was to determine the prevalence of phenotypic and genotypic extended spectrum β-lactamases (ESBLs) in 296 E. coli isolates recovered from diarrhoeic children younger than five years in Kano whose susceptibility profile against 7 antimicrobials had been determined. The E. coli isolates were subjected to double disc synergy test for phenotypic ESBLs detection and ESBL associated genes (blaCTX-M, blaTEM and blaSHV) were detected using conventional PCR. Phenotypically, 12.8% (38/296) E. coli isolates presented a ESBLs phenotype, with a significantly higher proportion in isolates from females compared with males (P-value = 0.024). blaCTX-M 73.3% and blaTEM 73.3% were the predominant resistance genes in the ESBLs positive E. coli (each detected in 22/30 isolates, of which 14 harboured both). In addition, 1/30 harboured blaCTX-M + blaTEM + blaSHV genes simultaneously. This study demonstrates the presence of ESBLs E. coli isolates in clinically affected children in Kano, and demonstrates the circulation of blaCTX-M and blaTEM associated with those phenotypes. Enactment of laws on prudent antibiotic use is urgently needed in Kano.