Rotavirus infection is a major cause of diarrheal illness and hospitalization in children <5 years old in Kenya and has been described in various settings and locations across the country and for different time points. In this study, we expand on the molecular characterization of rotavirus strains collected in Nairobi and Kisumu, Kenya, between 2000 and 2002. Rotavirus strains were typed by reverse-transcription polymerase chain reaction and characterized using VP6 monoclonal antibodies and RNA electrophoresis of the viral genome. A large proportion of specimens could not be genotyped; 41% did not produce a G type result, and 43% did not produce a P type result. Of the strains that could be genotyped, G1P[8] strains were predominant, followed by G2P[4] strains. In addition, G8 and G9 strains were seen in similar proportions Interestingly, the G and P combinations were more diverse among G8 and G9 rotavirus strains, suggesting the recent introduction of these strains into the human population. These observations are a link between the occasional observation of G8 and G9 strains at the turn of the century and the high predominance of G9P[8] strains observed in Kenya in 2005.