Leptospirosis is a zoonotic disease caused by a bacteria of the genus Leptospira. Climate is key in order to understand leptospirosis dynamics. El Niño 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 Niña and El Niño episodes in Colombia at three spatial scales in the period between 2007 and 2015.A cross-sectional retrospective study was performed.correlation and lagged cross correlation between time series of Oscillation Niño 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 Niño and Neutral periods with La Niña.At the national level, monthly number of cases raised a 25% during La Niña and decreased of 17% during El Niño. 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 Niña months. Of those, seven presented also an increase of cases during El Niño months and eight have a significant negative correlation with ONI.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.