Rectal swabs were collected from 1354 children <5 years of age with diarrhea attending Manhiça District Hospital and from 227 healthy community controls. Shigellosis incidence was high among children aged 12-47 months (488.4/10 child-years at risk). Fever and dysentery were prominent clinical findings. Shigella was more frequently isolated from cases than controls (6.7% versus 0.4%, P = 0.004), and from dysentery than nondysenteric diarrhea (24.1% versus 3.5%, P < 0.001). Shigella flexneri 2a, S. sonnei, and S. flexneri 6, were the most prevalent serotypes. © 2007 Lippincott Williams & Wilkins, Inc.