To determine the distribution of rotavirus strains and facilitate vaccine policy decisions in Taiwan, active hospital-based gastroenteritis surveillance was conducted in three sentinel hospitals. From 1 January 2005 to 31 December 2007, a total of 3435 children less than 5 years old with gastroenteritis were enrolled. The presence of rotavirus was documented by enzyme immunoassay (EIA), and the G and P genotypes were determined by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing methods. Results confirmed that 856 (25%) of these gastroenteritis admissions were EIA-positive for rotavirus and 448 (52%) of the rotavirus positive admissions were less than 2 years old. The most prevalent rotavirus genotypes were G1P[8] (40%), followed by strains G3P[8] (27%), and G9P[8] (17%). These data will help inform decisions as to whether rotavirus vaccine should be considered for inclusion into Taiwan's National Immunisation Programme.