Transfusion transmitted malaria is one of the most common transfusion transmissible infections and is a threat to blood safety and malaria control in Sub-Saharan African countries where malaria is endemic. The majority of healthy adults living in malaria endemic areas have some degree of immunity to the disease and an asymptomatic low-level parasitaemia is known to exist in a subset of this population. Blood donors recruited from the population are screened using a donor-selection criteria that includes age, weight, self-declared well-being and measurement of vital signs but not history of recent malaria infection or treatment. The Kenya National Blood Transfusion Services does not currently screen donated blood for malaria, opting instead for prophylactic anti-malarial use. This policy is inconsistent with the current WHO guidelines for the prevention of transfusion transmitted malaria, and the national policy guiding malaria treatment which states that antimalarial use is reserved for laboratory confirmed cases. A cross-sectional survey was conducted at two regional blood transfusion centres of differential malarial endemicity to determine the prevalence of malaria in blood donors. Of the 1,100 donors who participated in this study, five donors tested positive for malaria antigen, 3 from the Mombasa RBTC and 2 from the Nairobi RBTC giving an overall prevalence of 0.5% malaria antigen positivity. Only one peripheral blood film examined was positive for malaria yielding a total prevalence of 0.1% slide positivity. The prevalence of malaria in blood donors does not justify the routine use of prophylactic anti-malarias with each transfusion and a blood donor malaria screening algorithm as an alternative to malaria prophylaxis in the prevention of transfusion transmitted malaria should be developed and implemented.