In Colombia, undifferentiated tropical febrile illness (UTFI) are frequent and of considerable concern. They also share many clinical features. Between 2012 and 2013 in an endemic tropical area of Cordoba, Colombia, we conducted a prospective study to establish an etiological diagnosis of UTFI. Using diagnostic tests for dengue, leptospirosis, hantavirus, malaria, rickettsia, brucellosis, hepatitis A and B on 100 patients recruited for the study. We identified 69 patients with presumed UTFI: leptospirosis (n = 27), dengue (n = 26), hantavirus infection (n = 4), malaria (n = 4), rickettsial infection (n = 2), hepatitis A (n = 1), and brucellosis (n = 1); no hepatitis B cases were detected. Co-infections with malaria and leptospirosis (n = 1), hepatitis A and dengue (n = 1), hantavirus and dengue (n = 1), hantavirus, dengue, and leptospirosis (n = 1) were also identified. No etiologic agent was identified for 31 patients. We conclude that other etiologic agents besides dengue virus deserve greater attention by physicians and public health authorities in tropical area of Colombia.