Group A rotaviruses (RVA) are a major cause of acute gastroenteritis in children ≤ 5 y worldwide which could be prevented with two recently introduced vaccines - monovalent Rotarix (live-attenuated G1P[8] strain) and pentavalent RotaTeq (human-bovine reassortant containing serotypes G1, G2, G3, G4 and P[8]). Prior to implementation of vaccines into national immunization program we aimed to describe RVA genotype distribution in hospitalized children aged < 5 y in Estonia during 2007-2008. A total of 671 children with confirmed RVA gastroenteritis from three major pediatric hospitals were prospectively enrolled. G- and P-genotypes were detected from 124 stool samples by semi-nested reverse transcription-PCR. Severity of disease was assessed using Clark scoring system. The majority of cases (65%) occurred in infants aged 7 to 24 mo and were of moderate severity (mean Clark score 12.1 (SD 3.2)). The prevailing strain was G2P[4] (34.7%), causing significantly more cases than G4P[8] (12.9%), G1P[8] or G9P[8] (both 4.0%), G3P[8] (1.6%). Yearly differences in genotype distribution occurred, as G2P[4] (52.8%) dominated in 2007, but G4P[8] (26.9%) in 2008. One third of strains remained non-typeable. The distribution of RVA genotypes in Estonia differs from that seen in other Central and Eastern European countries, although one should bear in mind the large proportion of P-untypeable strains and natural fluctuations of dominating RVA genotypes. Nevertheless, considering the high genotype-independent efficacy of the vaccines, introduction of national immunization should be considered.