- Background Rotavirus vaccines were licensed in Israel in 2007, and in 2011 the pentavalent-vaccine (RV5) was introduced into the Israeli National Immunization plan. Aim To determine the effect of rotavirus-vaccines on the incidence of hospital visits due to rotavirus gastroenteritis (RVGE) and all-cause diarrhea in Jewish and Bedouin children <5 year residing in southern Israel. Methods We conducted a population-based, prospective, observational study. Data from 2006 through 2013 were analyzed. Our hospital is the only medical center in the region, enabling age-specific incidences calculation. Results In the pre-vaccine period, the overall RVGE hospital visits rates per 1000 in children <12, 12–23 and 24–59 m were 16.1, 18.6 and 1.4 in Jewish children, respectively. The respective rates in Bedouin children were 26.4, 12.5 and 0.7 (P < 0.001 for <12 m). Hospitalization rates were higher among Bedouin than among Jewish children (60.0% vs. 39.7%, P < 0.001). Vaccine uptake was faster in the Jewish vs. the Bedouin population. In the year following RV5 introduction, RVGE hospital visits rates declined by 82%, 70% (P < 0.001 both) and 36% (P = 0.092) in Jewish children <12, 12–23 and 24–59 m, respectively. In Bedouin children, the respective RVGE rates declined by 70% (P < 0.001), 21% (P = ns) and 14% (P = ns). Throughout the study, RVGE rates declined significantly in children <12, and 12–23 m by 80% and 88% in Jewish children, respectively, and by 62 and 75% in Bedouin children, respectively (P < 0.001 for all declines). In children 24–59 m, RVGE rates declined by 46% (P = 0.025) in Jewish children, but no reduction was observed in Bedouin children. The dynamics of all-cause diarrhea rates were similar to that of RVGE. Conclusions Significant reductions of RVGE rates were observed, following Rota-vaccine introduction in southern Israel in both Jewish and Bedouin children. However, the impact was faster and more profound in Jewish children, probably related to higher vaccine uptake and possibly to lifestyle differences.