Between 2007 and 2009, active surveys were conducted on backyard poultry (chickens, guinea fowls and ducks) in four areas of Côte d'Ivoire, including two areas where avian influenza H5N1 outbreaks occurred in 2006. Each bird underwent clinical examination. In total, 5,578 sera, 4,580 tracheal swabs and 5,120 cloacal swabs were collected, plus tissues from 35 sick chickens. Using the haemagglutination inhibition (HI) test, 277 and 36 serum samples were positive for H5 and H7, respectively; all were negative for H9. All samples were negative by reverse transcription polymerase chain reaction. These results confirm the circulation of H5 and H7 influenza subtypes in backyard poultry in Côte d'Ivoire. Given that the seropositive birds were healthy, the circulating subtypes may be low pathogenicity avian influenza strains. Half (2,680) of the sera collected from chickens were tested by HI for Newcastle disease virus (NDV) antibody: 531 were positive. The seroprevalence of 19.8% confirms the endemic status of NDV, but may underestimate its true prevalence in Côte d'Ivoire.