On the island of Madagascar, malaria was nearly eradicated in the highland areas and malaria transmission was significantly decreased in the coastal areas between the 1940s and 1960s. The success of the control programme was primarily achieved by chloroquine (CQ) use at the community level. CQ was administered to children weekly on a routine basis for malaria prevention in the period 1949-1971. Then, the Malagasy Government was unable to financially support the malaria control programme. The malarial situation worsened in the 1980s, partly due to the shortage of CQ. A malaria epidemic occurred. To deal with this epidemic, massive CQ use was urgently adopted. CQ has remained the first-line drug since 1945, but the prevalence of Plasmodium falciparum carrying the pfcrt mutation associated with CQ resistance remains low (<3%). However, late CQ treatment failure has been reported and the prevalence may be as high as 35% during 14-day follow-up since 1982. In an effort to eliminate malaria as a public health problem, a shift from CQ to artemisinin-based combination therapy has been advocated by a new policy since December 2005. A change of this kind is complex and the lessons learnt from the six decades of CQ use are of the utmost importance to achieve malaria control.