We aimed at characterizing commercial and traditional village poultry farming in Mali, with a focus on practices influencing the risk of transmission of avian influenza and Newcastle disease. Surveys were conducted in 2009–2011 in a study area covering approximately 98% of the Malian poultry population. Among the 282 commercial farms investigated, of which 64 had not been known by the government authorities, 83% were located within a 50 km radius from the capitals of the country and regions and 54% had low biosecurity standard. Among the 152 randomly selected village household flocks investigated, characteristics were overall similar to those in other African countries but some differences were notable including a large flock size (median 44 poultry), a low presence of ducks and geese (11% and 1.1% of flocks, respectively), vaccination against Newcastle disease being common (49% of flocks), a low proportion of households selling sick and dead birds (0.7% and 0%, respectively) and limited cohabitation between poultry and humans at night. Our recommendations to limit the risk of disease transmission include (1) for commercial farms, to introduce compulsory farm registration and accreditation, to increase technical proficiency and access to credit for farms with low biosecurity, and to support poultry producer associations; (2) for village poultry, to promote better quarantine and management of sick and dead birds. Such detailed knowledge of country-specific characteristics of poultry production systems is essential to be able to develop more efficient disease risk management policies.