Studies on the health benefits of exclusive breastfeeding (EBF) and susceptibility to malaria have shown contradictory results. These studies often failed to account for dose response effects. The deuterium dilution technique was used to evaluate the breast milk intake, the amount of water from sources other than human milk and the exclusivity of breastfeeding. We determine Plasmodium falciparum parasitaemia prevalence in children aged less than six month according to their breastfeeding regimen and maternal milk dose ingested in southern Benin. We conducted a cross sectional study in the Ouidah Kpomasse Tori-Bossito (OKT) health zone in southern Benin from February to December 2014, an intense transmission season. 115 mothers paired with their children aged from 0 to 6 months were enrolled. The daily human milk was measured through saliva of each mother and child pair (MCP) over a period of 14 days by the technique of deuterium oxide "dose to the mother" using the Fourier Transformed Infrared Spectrometer (FTIR). Malaria parasitaemia in children was determined by quantitative Polymerase Chain Reaction (qPCR) in real time at day 14 and day 28. The average age was 2.3 months. The distribution of Plasmodium falciparum parasitaemia in children was 0.00%, 5.08% and 3.85% respectively in exclusive, predominant and partial breastfeeding regimens. The mean intake of breast milk was 641.71 mL per day; 256.75 mL of water per day was taken from sources other than breastmilk. Adjusted linear regression analysis revealed a significant association between quantity of breastmilk and parasitaemia prevalence; infected children (qPCR positive) had 164.11 mL of ingested breastmilk per day less than children without parasitaemia (p=0.00). Our findings highlighted the association between the low risk of Plasmodium falciparum parasitaemia and the ingested breastmilk dose. Study with larger numbers of patients would be necessary to confirm this relationship.