In the present study, we compared Trypanosoma cruzi infection in four native mammals from a hyperendemic area of Chagas disease in Chile for two different periods to assess the occurrence of interannual variation (1999-2000 vs. 2005-2006). Parasite detection in mammals is performed by polymerase chain reaction assays and confirmed by Southern blot analysis and hybridization test with a universal probe. Results showed significant differences in the levels of T. cruzi infection between the compared periods. We suggest that the major El Niño event occurred in 1997-1998, a large-scale global climatic fluctuation, could be indirectly explaining the extremely high T. cruzi infection in 1999-2000 by means of a time-lag response of the wild transmission cycle of Chagas disease in semiarid Chile after the irruption of small rodent populations.