Abstract The aim of this study was to evaluate the association between bartonellosis and selected climatic factors during the time periods 1983–1988 and 1995–99, which included two events of the El Niño phenomenon (1986–88,1997–98), and to identify a reliable climate parameter to be used as an alert indicator for bartonellosis outbreaks in Ancash. The study site was Ancash and its province Carhuaz, Peru. Time-series cross-correlation analysis was used to assess the association between bartonellosis and climate parameters. A higher, almost 4-fold, monthly bartonellosis incidence risk in Ancash department was observed during the El Niño events of 1986–88 and 1997–98. At a regional (Ancash department) and local level (Carhuaz, Ancash), the best correlation was observed between bartonellosis and sea-surface temperature (SST). The results indicate that SST would be the best climate parameter to be used as an alert indicator for bartonellosis outbreaks in Ancash.