BackgroundMalaria intermittent preventive treatment of malaria in infant with sulphadoxine-pyrimethamine (IPTi-SP) reduced the incidence of malaria and anaemia by 30% and 20% respectively. The strategy is now a recommended policy for malaria control. However, there was no published study on the impact of the strategy on mortality. The present study assessed the impact of the implementation of IPTi-SP in health services in Mali on all-cause mortality.MethodsThe 22 health sub-districts of the district of Kolokani were randomized at a 1:1 ratio to either receive IPTi-SP or to serve as a control. The IPTi-SP was implemented for two years starting December 2006. Information on births and deaths through 31 March, 2009 was collected on all children who reached four months of age on 1 December, 2006, likely to be exposed to the intervention in 75 localities randomly selected in each zone.ResultsA total of 5,882 children (2,869 from the intervention zone and 3,013 from the nonintervention zone) who reached four months of age between 1 December, 2006 and 1 December, 2008 were surveyed between the age of four months to the age of 18 months from 1 December, 2006 to 31 March, 2009. In the cohort of four to 18 months of age, the mortality rate per 1,000 children was 2.53 in the intervention zone compared to 3.46 in the nonintervention zone, gender and season adjusted mortality rate ratio (MRR) = 0.73 (95% CI 0.55-0.97, p = 0.029). In the cohort of the four to 12 months of age, mortality rates per 1,000 children were 2.22 in the intervention zone and 3.13 in the non-intervention zone, MRR = 0.71 (95% CI 0.49-1.02, p = 0.064) adjusted for gender and season.ConclusionThe implementation of the IPTi-SP resulted in a substantial reduction in all-cause mortality in children. The results of this study support the adoption and the implementation of IPTi-SP as malaria control strategy.Trial RegistrationClinicalTrials.govNCT00766662