Rotavirus gastroenteritis (RV GE) is a leading cause of diarrhoea in young children. The purpose of this epidemiological surveillance was to measure the disease burden of RV GE among children <5 years of age in two regions of Switzerland, Geneva and Lucerne. One hospital and four paediatricians participated per region. The surveillance lasted from December 2006 to June 2007. The population denominator for calculation of the RV GE incidence rate was the average of the overall study population <5 years of age under surveillance during the surveillance period. At the study sites, 513 children with GE were presented. Stool sample was collected and examined in 341 cases, of which 130 were RV positive (38.1%). Informed consent to participate in the study was obtained for 113 RV positive subjects. The overall RV GE incidence rate was 0.97% in Lucerne [lower incidence interval (LCI), 0.71%; upper incidence interval (UCI), 1.2%] compared with 0.65 and in Geneva (LCI, 0.50%; UCI, 0.81%). Disease severity assessments using the Vescari score showed that the RV GE episodes were more severe in Lucerne than in Geneva (14.05 +/- 3.05 vs 12.85 +/- 2.87), which was confirmed by a higher hospitalisation rate in Lucerne at the study visit (82.9% vs 23.6%). More children had fever in Geneva than in Lucerne (42.9% vs 26.8%), and more children were hospitalised during the follow-up period in Geneva than in Lucerne (14.5% vs 2.5%). Genotyping of RV positive stool samples revealed that both G1 and P8 were the most prevalent types in both regions. There was a statistically significant difference in the distribution frequency of G1 between the two regions (p = 0.039). Assessment of health economic data confirmed the economic burden of RV GE episodes. In conclusion, RV GE episodes are a health burden as well as an economic burden also for the children in a developed country such as Switzerland.