Background: Rotavirus is a major cause of gastroenteritis in children worldwide, but there is no data available on the incidence of rotavirus gastroenteritis or on the strains circulating in Portugal. Methods: We determined prospectively the incidence of rotavirus infection in non-hospitalised children and the genotypes circulating during one winter season in the central region of Portugal. Results: Rotavirus was found in 45% of the samples tested. The peak incidence was in February (54% positive) and March (60% positive). Genotyping was performed in 195 samples; unexpectedly, G9P was present in 90% of the cases, a much higher percentage than previously reported in other countries. Conclusions: These results contribute to the assessment of the burden of disease attributable to rotavirus in Portugal and facilitate preparation for intervention by vaccination. The predominance of G9 in Portugal is unlikely to be a local phenomenon, and may be observed elsewhere in Portugal and Europe. The epidemiology of rotaviruses in Portugal should be monitored in subsequent years.