Infection with Shigella is considered a major cause of morbidity and mortality in children with diarrhea in developing countries, especially in Iran. Due to the importance of country-level epidemiological data, molecular characterization of genetic determinants of Shigella spp. is a necessity. The aim of the present study was to investigate the prevalence of integron types, bla-CTX-M, bla-SHV and blaTEM β-lactamase genes of Shigella isolates in pediatric patients in Tehran, Iran. In a time period of 18 months from May 2015 to August 2017, 75 Shigella spp. were isolated from non-duplicative diarrheal stool specimens in six different hospitals in Tehran. The isolates from patients were further analyzed for their antibiotic susceptibility and extended-spectrum beta-lactamase (ESBL) production. Polymerase chain reaction was performed for amplification of the integrons (I, II, III), TEM, SHV, CTX-M15. The prevalence of S. sonnei, S. flexneri, S. dysenteriae and S. boydii were 40 (53.3%), 33 (44%), 1 (1.3%) and 1 (1.3%), respectively. The results of an antimicrobial resistance test showed that the high percentage of resistance to nalidixic acid (NA), ampicillin (AMP) and trimethoprim/sulfamethoxazole (SXT) included 38 (50.6%), 59 (81.3%) and 64 (88%) isolates, respectively. Further results revealed that 52% and 76% of Shigella isolates carried intI and intII genes, respectively. In this study, the rates of CTX-M (10.7%), SHV (28%) and TEM (21.3%) were determined, all of which were positive for blaCTX-M15. This study showed the high prevalence of multidrug resistant S. sonnei and S. flexneri. Furthermore, it highlighted the increasing integrons (intI and intII) and ESBL genes, especially blaCTX-M15, in Shigella isolates.