Background Several factors, including environmental and climatic factors, influence the transmission of vector-borne diseases. Nevertheless, the identification and relative importance of climatic factors for vector-borne diseases remain controversial. Dengue is the world's most important viral vector-borne disease, and the controversy about climatic effects also applies in this case. Here we address the role of climate variability in shaping the interannual pattern of dengue epidemics. Methods and Findings We have analysed monthly data for Thailand from 1983 to 1997 using wavelet approaches that can describe nonstationary phenomena and that also allow the quantification of nonstationary associations between time series. We report a strong association between monthly dengue incidence in Thailand and the dynamics of El Niño for the 2–3-y periodic mode. This association is nonstationary, seen only from 1986 to 1992, and appears to have a major influence on the synchrony of dengue epidemics in Thailand. Conclusion The underlying mechanism for the synchronisation of dengue epidemics may resemble that of a pacemaker, in which intrinsic disease dynamics interact with climate variations driven by El Niño to propagate travelling waves of infection. When association with El Niño is strong in the 2–3-y periodic mode, one observes high synchrony of dengue epidemics over Thailand. When this association is absent, the seasonal dynamics become dominant and the synchrony initiated in Bangkok collapses., In Thailand, dengue transmission patterns are complex, with El Nino showing an association with some epidemics only; other reasons will need to be found for the initiation of other outbreaks