OBJECTIVE: Establishing seroprevalence against Bartonella and Babesia microti in arural population exposed and/or non-exposed to domestic animals in Cordoba,Colombia. METHODOLOGY: Sera samples taken from 80 people from Montería and Cereté (Córdoba department) were analysed; the population sample was chosen by non-probabilistic means. Anti-Bartonella and Babesia microti were detected by indirect immunofluorescence (IFI), (Focus Technologies, Cypres, CA, USA). RESULTS: Total anti-bartonella IgG seroprevalence was 48,7 % (39/80), 77 % being male and 23 % female. Bartonella quintana seropositivity was 45 % (36/80) and Bartonella henselae seropositivity 30 % (24/80); 21 of these individuals (26,2 %) had antibodies to both bartonellas. Babesia microti seroprevelence was 30,6 % (23/80),65 % being male patients. CONCLUSIONS: High Bartonella and Babesia seroprevelence showed that infection levels had been underestimated in Colombia. Medical and sanitary authorities on the Caribbean coast of Colombia must take measures for monitoring the distribution,propagation and identification of human populations at risk of contracting infection by these micro-organisms and also orientate diagnosis and enable suitable prevention strategies to be developed for these diseases.