INTRODUCTION: Leptospirosis is a zoonotic disease caused by a bacteria of the genus Leptospira. Climate is key in order to understand leptospirosis dynamics. El Nino Southern Oscillation is the main modulator of climate in Colombia. Our goal was to analyze the changes that occurred in number of cases and incidence rate of leptospirosis during La Nina and El Nino episodes in Colombia at three spatial scales in the period between 2007 and 2015. METHODOLOGY: A cross-sectional retrospective study was performed. DATA ANALYSIS: correlation and lagged cross correlation between time series of Oscillation Nino Index and time series of standardized number of leptospirosis cases; construction of annual cycle of leptospirosis; comparison of changes of number of cases between Neutral, periods with El Nino and Neutral periods with La Nina. RESULTS: At the national level, monthly number of cases raised a 25% during La Nina and decreased of 17% during El Nino. At departmental level, increase of cases in both phases of ENSO, depending on the location in the country, was found. At the municipal level, 17 have a rise in the number of cases during La Nina months. Of those, seven presented also an increase of cases during El Nino months and eight have a significant negative correlation with ONI. CONCLUSIONS: In Colombia, there exists a relationship between leptospirosis and the excess and lack of rainfall related with ENSO. The contrasting results from each spatial scale, reinforce that leptospirosis is a multidimensional disease with high complex interactions among its determinants.