Culture and immunomagnetic separation-polymerase chain reaction assays (IMS-PCR) were used to isolate and identify Shigella flexneri, S. dysenteriae type I and S. sonnei in faeces from 250 children up to 5 years and from their mothers (n = 143) selected at random from a large urban marginal community of Costa Rica. Children hospitalized because of severe diarrhoea (n = 110) were also studied. Only S. flexneri, mainly serotype 2a, and S. sonnei were found by culture. All specimens in which Shigella was cultured were also positive by the corresponding IMS-PCR. S. flexneri was isolated by culture from 1 (0.7%) mother and 4 (1.6%) community children. S. sonnei was found in 2 (0.8%) children. An additional 12 S. flexneri and four S. sonnei in the community children were found by IMS-PCR. In total, Shigella was cultured from 0.7% of mothers and 2.4% of children. By the IMS-PCR 2% of mothers and 8% of children were positive. S. flexneri was isolated by culture from 14 (12.7%) hospitalized children and S. sonnei from 1 (0.9%). An additional 11 S. flexneri and three S. sonnei were found by IMS-PCR. In total, Shigella was cultured from 13.6% of hospitalized children. By the IMS-PCR 26% of them were Shigella positive. Thus IMS-PCR was more than twice as effective in diagnosing shigellae as culture. Twelve (60%) Shigella positive community children were above 3-years-old and 25% of them were under one year. Seven (35%) of the Shigella positive children had dysenteric and 9 (45%) normal stools. Half of the Shigella infected community children had been weaned before the 3 months of age. By the age of 5 months, 90% of them were already weaned. Seventeen (59%) of the hospitalized Shigella positive children were under 1 year of age. The stools were watery or semiliquid in 13 (45%) and dysenteric in 12 (41%) of them. We conclude that shigellosis is common in Costa Rica and represents an important cause of severe infant diarrhoea requiring hospitalization.