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Introduction: Leptospirosis represents a public health problem and is a significant cause of morbidity and mortality in the region of Uraba. However, its notification reveals diagnostic limitations. Objective: To establish the incidence of leptospirosis in the municipalities of the Eje Bananero of the Uraba region, to describe the magnitude of under registration, and to propose guidelines for laboratory diagnosis by the public health network. Materials and methods: Two leptospirosis information sources were used: national official surveillance system and a cross-sectional study of 479 acutephase patients since April 2010 to May 2012. The diagnosis was made using three different tests: indirect immunofluorescence, micro agglutination test and blood cultures. Exhaustivity percentage of each information source was performed by capture and recapture test. Results: Leptospirosis was confirmed in 58% at least by one and 10.43 % of cases were positive by all three methods. Inclusion of a native strain in the MAT panel increased the percentage positivity by 15%. The cumulative incidence rate was 66.5/100,000 inhabitants and the case fatality ratio were 2.15%. The underreporting rates of leptospirosis in the Uraba region were 27.8% in morbidity and 66.6% in mortality. Conclusion: The under registration of leptospirosis in the region highlights the necessity to use more than one diagnostic test to identify Leptospira in patients from endemic areas. This under registration could be a common situation throughout the country. [ABSTRACT FROM AUTHOR]