BACKGROUND Rotavirus infections account every year in Chile, for approximately 53,000 emergency consultations and 8,000 hospital admissions among children under three years of age. AIM To estimate incidence rates of severe rotavirus gastroenteritis in children <3 years of age, living in the V and VIII Regions and to identify the predominant viral serotypes. MATERIAL AND METHODS A prospective hospital-based surveillance for severe gastroenteritis was implemented in public and private hospitals of Viña del Mar and Valparaiso (Region V) and of Chiguayante, Concepción, Penco, San Pedro de la Paz, Talcahuano and Tomé (Region VIII). All children <3 years of age residing in the districts, who consulted for severe gastroenteritis requiring oral or intravenous rehydration (equivalent to WHO plan B or C), or who were admitted to the hospital, were enrolled. Demographic and clinical information and a stool sample were obtained. Rotavirus was detected by ELISA and positive samples were serotyped by ELISA or real time PCR. RESULTS Between January 23 and June 30, 2003, a total of 760 children were recruited. Among these, 343 (45%) were admitted to the hospital. Stool samples were collected from 433 children. Among these, 214 were positive for rotavirus (49.4%). Overall, monthly disease incidence rates were 124/100,000 in V Region, and 114/100,000 in VIII Region. The predominant serotype was G4. CONCLUSIONS Rotavirus was responsible for nearly half of the severe gastroenteritis episodes among children <3 years, during a predominantly G4 serotype season. Every year, approximately one every 70 children <3 years will have a severe rotavirus gastroenteritis episode.