It has been found that Kawasaki disease (KD) cases diagnosed in Japan, Hawaii and San Diego, USA increase when tropospheric wind patterns arrive from central Asia, suggesting a common, wind-borne causal agent. We analyzed KD cases hospitalized in Santiago, Chile to look for associations with local, regional and large scale meteorological variables. We compiled monthly data of KD incidence rates, local meteorological variables, large scale wind patterns and several El Niño Southern Oscillation (ENSO) indices for 2001–2010; we considered standardized anomalies in all analyses and used linear time series models to account for data autocorrelation. We found that meteorological variables explain 38% of variance in KD rates. A unit increase in northerly wind at 3 lagged months, temperature at 1 and 3 lagged months and monthly change of ENSO 4 index are associated with changes in KD rates of 0.203 (95% CI 0.049–0.358), 0.181 (95% CI 0.014–0.347), 0.192 (95% CI 0.030–0.353) and − 0.307 (95% CI − 0.458–0.156), respectively. These results are robust when northerly wind level is changed or when a shorter period (2005–2010) is used to estimate model parameters. We found a statistical association of KD at Santiago, Chile with tropospheric, northerly wind patterns suggesting that dust transported from the Atacama Desert could include a causative agent. A novel result is that ENSO dynamics also explain part of KD variability with a decrease in KD when La Niña is dissipating or El Niño is on the rise; hence climate scale dynamics might be taken into account in future studies worldwide — at least as a potential explanatory variable that may confound KD seasonality on a global scale.