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We present a large-scale study of the relationships between selective logging and forest phenology in the Brazilian Amazon. Time-series analysis of MODIS satellite data of selectively logged forests in Mato Grosso, Brazil, shows that relatively low levels (5–10%) of canopy damage cause significant and long-lasting (more than 3 years) changes in forest phenology. Partial clearing slows forest green-up in the dry season, progressively dries the canopy, and induces overall seasonal deficits in canopy moisture and greenness. Given large and increasing geographic extent of selective logging throughout Amazonia, this phenological disturbance has a potential to impact carbon and water fluxes, nutrient dynamics, and other functional processes in these forests.