Background: Dysentery accounts for a significant proportion of morbidity and mortality cases, especially in children with diarrhea in developing countries. Shigellosis remains a public health problem in Iran. Objectives: The objectives of this study were to investigate the presence and the frequency of Shigella spp. among children younger than 10 years with diarrhea and to determine the antimicrobial resistance patterns of these isolates in Tehran, Iran. Patients and Methods: This cross-sectional study was conducted in two pediatric hospitals in Tehran, from October, 2013 to October, 2014. Nine hundred and thirty-eight (n = 938) stool samples were collected (one stool per patient) from children less than 10 years of age. The stools were primarily cultured on MacConkey agar and xylose lysine deoxycholate (XLD). (Selenite-F broth is also used as an enrichment medium for the isolation of Shigella spp.) All of the isolates were confirmed as Shigella species by biochemical and serological tests. Molecular confirmation of Shigella isolates was determined by polymerase chain reaction (PCR) using specific primers for the ipaH gene. The antibiotic susceptibility of the Shigella isolates was tested using the Kirby-Bauer disc-diffusion method. Results: Amongst 938 stool samples, 36 were Shigella spp. S. sonnei (61.1%, n = 22), which was the most common, followed by S. flexneri (27.8%, n = 10), S. boydii (8.3%, n = 3), and S. dysenteriae (2.8%, n = 1). Furthermore, most Shigella isolates showed resistance to amoxicillin (83.3%), tetracycline (61.1%), and co-trimoxazole (83.3%). No resistance was found against ciprofloxacin and imipenem. This study showed that S. sonnei is currently the predominant species in Tehran, Iran. Conclusions: Because resistance to antibiotics changes constantly, Shigella strains should be under surveillance in order to monitor local susceptibility and subsequently formulate policies for the use of antimicrobial drugs.