BACKGROUND: In Africa, recent surveillance has demonstrated a high burden of influenza, but influenza vaccine is rarely used. In Kenya, a country with a tropical climate, influenza has been shown to circulate year-round, like in other tropical countries. METHODS: During three months in 2010 and 2011, and two months in 2012, the Kenya Medical Research Institute/CDC-Kenya offered free injectable trivalent inactivated influenza vaccine to children 6 months-10 years old in two resource-poor communities in Kenya - Kibera andLwak (total population ~50,000). We conducted a case-control study to evaluate vaccine effectiveness (VE)in preventing laboratory-confirmed influenza associated with influenza-like illness and acute lower respiratory illness. RESULTS: Of 52,000 eligible children, 41%, 48%, and 51% received at least one vaccine in 2010, 2011, and 2012, respectively; 30%, 36%, and 38% were fully vaccinated. VE among fully vaccinated children was 57% (95% CI = 29-74%) during a 6-month follow-up period, 39% (95% CI = 17-56%) during a 9-month follow-up period, and 48% (95% CI = 32-61%) during a 12-month follow-up period. For the 12-month follow-up period, VE was statistically significant in children < 5 years and children 5 years old < 10 years old (50% and 46%, respectively). CONCLUSIONS: In Kenya, parents of nearly half of eligible children under 10 years old chose to get their children vaccinated with a free influenza vaccine. During a 12-month follow-up period the vaccine was moderately effective in preventing medically attended influenza-associated respiratory illness.