Ninety-seven isolates of Shigella flexneri from children seeking medical care from three sites in Egypt were characterized. Overall, 46·4% of children (median age 17 months) were febrile or reported blood in their stools, 25·8% were dehydrated and 16·5% were admitted to hospital. Serotypes 2a (37·1%), 1b (18·6%), 1c (17·5%), and 6 (15·5%) comprised over 88·7% of the total isolates. We observed marked resistance to ampicillin (87·6%), tetracycline (84·5%) and trimethoprim–sulfamethoxazole (63·9%). Pulsed-field electrophoresis grouped the majority of isolates within a serotype together, separately from isolates of an alternative serotype. The set gene was present in all serogroup 2a isolates, however, the sen gene was detected in every isolate. Our results show S. flexneri 1c has emerged as a dominant S. flexneri serotype in Egypt. Development and application of a Shigella vaccine should consider the diversity of Shigella serotypes within a geographical region prior to administration.