In Peru, the climate pattern El Niño-Southern Oscillation (ENSO) was linked to a resurgence of cholera in 1998. While previous studies found a temperature connection, El Niño’s impact on cholera in Peru has not been fully explored. In this study, climate associations with cholera incidence during the 1997–1998 El Niño are examined at a district-level in Piura, a coastal area located in northern Peru. Piura is important to study because it was one of the most affected areas by cholera and El Niño in 1998. The approach taken in this study is a “multiple pathways” perspective, which highlights various dimensions of ENSO to explain cholera linkages. Associations were estimated at various temporal lags using bivariate regression and then mapped in ArcGIS. The results show significant cholera associations with SST in the central equatorial Pacific and on the coast (0–1 month lag), rainfall (1 month lag), and mean and maximum temperatures (5 month lags). Overall, the strongest consistent impact was rainfall, which supports the notion that flooding was a pathway for cholera exposure in Piura. Local sea and air temperature associations also suggest that exposure was potentially linked to vibrio proliferation, which increased the probability of cholera risk. Furthermore, this study shows that climate impacts on cholera were unevenly distributed across Piura, indicating that some districts were more vulnerable than others, possibly related to infrastructure deprivation. In conclusion, the study provides a basis for future investigations, which may be useful for epidemic preparedness during future El Niños and other extreme climate events. © 2014, Springer Science+Business Media Dordrecht.