The implementation of molecular and serological tests has led a great decline in transfusion-transmitted infections. Unfortunately, however, this has only occurred in high-income countries, whereas the scenario is different in low-income countries and in rural areas of middle-income countries, in which access to serological tests is sometimes not feasible or limited by economic factors1,2. Furthermore, in middle and low-income countries, the burden of infectious diseases tends to be higher and subjects are often weakened by various factors, including malnutrition. These factors result in a population that is more vulnerable and at increased risk of infections. Although the search for relevant pathogens that can be transmitted by blood transfusion is implemented worldwide, various pathogens that can be present in blood bank donations remain under studied, as in the case of some bacteria such as Leptospira spp. and Bartonella spp. Bartonella species are re-emerging blood-borne organisms, capable of causing prolonged infections in animals and humans3, while leptospirosis is recognised as an emerging public health problem worldwide4. Both infections are considered to be neglected tropical diseases. In humans, Bartonella spp. cause infections of varying severity, ranging from asymptomatic bacteraemia to severe cases with chronic manifestations responsible for persistent disease and death3. So far, various members of the Bartonella genus have been associated with human disease, the most relevant being Bartonella henselae, causing cat scratch disease, Bartonella quintana, causing trench fever, and Bartonella bacilliformis, the causal agent of Carrion’s disease2. This last micro-organism is endemic in Latin America, and specifically in the Andean valleys. B. bacilliformis infects red blood cells and endothelial cells and, as mentioned above, is the aetiological agent of Carrion’s disease, a biphasic disease with two different clinical presentations: an initial febrile phase with haemolytic anaemia, known as Oroya fever, which has a mortality rate ranging from 44–88% in untreated patients, and a second phase characterised by the development of dermal eruptions, known as “Peruvian wart”5. It is important to highlight the presence of asymptomatic people, who account for about 45% of the population in some endemic areas6; consequently, the risk of transfusion transmission is of note, especially because of the ability of B. bacilliformis to survive in blood stored at 4 oC for up to 1 year7. Leptospirosis is one of the most common bacterial zoonotic diseases worldwide. Various mammals such as rodents, livestock and domestic pets can act as reservoir hosts8. Traditionally, infection in humans is due to contact with Leptospira-contaminated sites in different environments: at work (veterinarians, farmers, sewer cleaners), in alleys and slums with poor drainage, and in recent years, during international travel and recreational activities9. Infection by Leptospira may be asymptomatic or may cause a mild influenza-like illness that can resolve spontaneously. Symptomatic infection may present as non-specific symptoms such as fever, chills, headache, myalgia and jaundice8. As mentioned above, the presence of asymptomatic carriers may favour the risk of transfusion-related transmission. The distribution of Carrion’s disease is limited to the Andean valleys, while leptospirosis occurs worldwide, being more common in tropical and subtropical regions due to the wet weather. Rainfall, flooding and climatic phenomena, such as “El Nino”, increase the risk of these bacterial infections4. There is no information about the prevalence of these bacteria in blood donors in Peru. Moreover, analyses to detect the presence of Leptospira spp. are not routine in this country and the presence of B. bacilliformis is only tested for in blood banks in endemic areas, but not in the remaining ones, irrespectively of whether there are inhabitants arriving from or travelling to endemic areas10,11. This represents a health problem, since subjects receiving a blood transfusion are usually immunocompromised and more vulnerable to the development of severe infectious diseases from potentially transfusion-transmitted micro-organisms. The aim of the present study was to examine the prevalence of Bartonella spp. and Leptospira spp. in blood donors in Cajamarca, in northern Peru, and describe the associated epidemiological factors.