Rotaviruses (RV) are major causative agents of acute gastroenteritis (AGE) requiring hospitalization in children; RV hospitalizations may be largely eliminated by universal mass vaccination with RV vaccine. We conducted a hospital-based prospective survey of AGE in children over 2 RV epidemic seasons, from 2006 to 2008, when the coverage of RV vaccination in Finland increased to 35% of the birth cohort. RVs were detected by reverse transcription polymerase chain reaction (RT-PCR). In the first season, only 38% of AGE cases were RV-positive, and the onset of the RV season was delayed. Type G1P[8], RVs accounted for 40%, G2P[4] for 19%, G3P[8] for 2%, G4P[8] for 2% and G9P[8] for 38%. In the second season, 63% of AGE cases were RV-positive: G1P[8] accounted for 73%, G2P[4] for only 3%, G3P[8] for 4%, G4P[8] for 13%, and G9P[8] had almost disappeared. G2P[4] RV did not become predominant at the coverage level of 29% of G1P[8] human RV vaccine. RV-associated hospitalizations were seen in children up to the age of 9 y. This study forms the epidemiological background for the follow-up of the impact of universal RV vaccination in Finland introduced in 2009.