The depth of the root system controls the maximum amount of soil water that can be transpired by the vegetation into the atmosphere during dry periods. Water uptake from deep soil layers has been found to contribute significantly to the dry season transpiration at some sites in Amazonia and it has been estimated that large parts of the evergreen forests in Amazonia depend on deep roots to survive the dry season. Thus, the presence of deep roots might provide a significant source of atmospheric moisture during the dry season, and one which would be affected by deforestation. We investigate the role of deep-rooted vegetation and its removal in the context of Amazonian deforestation using an atmospheric General Circulation Model (GCM). A distribution of deep roots is obtained by a numerical optimization approach. The simulated climate with the use of the calculated deep roots substantially improves the seasonal characteristics of the GCM. Three additional simulations are then conducted in order to isolate the effect of rooting depth reduction from other parameter changes associated with large-scale deforestation. Most of the climatic effects occur during the dry season and are attributed to the reduction of rooting depth. Dry periods are found to last longer, being more intense with drier and warmer air, while the wet season remains fairly unchanged. The implications of these climatic effects for the re-establishment of the natural evergreen forest are discussed.