Using the data of National Center for Environmental Prediction (NCEP) Reanalysis, the Climate Prediction Center Merged Analysis of Precipitation (CMAP), the Tropical Rainfall Measuring Mission (TRMM) and meteorological station observations, it was found that the two study areas reside in different climate regimes. The precipitation in Cusco, which is located at the eastern tropical-subtropical Andes, is strongly influenced by the South American summer monsoon (SASM) activities over the eastern continent. The rainfall in Caraz, which is only about 5° north of Cusco but situated in the western tropical Andes, shows much weaker correlation with SASM rainfall variations. Distinct characteristics of climatic risk factors in each area are also distinguished in this paper. During the 1997/98 El Niņo event, more rainfall and higher temperature were observed in Caraz, while only the local air temperature increasing is significant in Cusco. The predictive ability of key climatic factors over the equatorial central-eastern Pacific is also assessed. Data on disease incidence at Caraz and the large-scale tropospheric mean temperature shows strong correlation, where the temperature leads the disease epidemic two months. A similar result also was obtained from the lag-correlation with the large-scale precipitation in this area. Further investigation on land surface processes to determine the lower boundary conditions that influence the local climate and ecology variations is on going.