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Despite a large increase in the area of selectively logged tropical forest worldwide, the carbon stored in deadwood across a tropical forest degradation gradient at the landscape scale remains poorly documented. Many carbon stock studies have either focused exclusively on live standing biomass or have been carried out in primary forests that are unaffected by logging, despite the fact that coarse woody debris (deadwood with ≥10 cm diameter) can contain significant portions of a forest's carbon stock. We used a field-based assessment to quantify how the relative contribution of deadwood to total above-ground carbon stock changes across a disturbance gradient, from unlogged old-growth forest to severely degraded twice-logged forest, to oil palm plantation. We measured in 193 vegetation plots (25 × 25 m), equating to a survey area of >12 ha of tropical humid forest located within the Stability of Altered Forest Ecosystems Project area, in Sabah, Malaysia. Our results indicate that significant amounts of carbon are stored in deadwood across forest stands. Live tree carbon storage decreased exponentially with increasing forest degradation 7–10 years after logging while deadwood accounted for >50% of above-ground carbon stocks in salvage-logged forest stands, more than twice the proportion commonly assumed in the literature. This carbon will be released as decomposition proceeds. Given the high rates of deforestation and degradation presently occurring in Southeast Asia, our findings have important implications for the calculation of current carbon stocks and sources as a result of human-modification of tropical forests. Assuming similar patterns are prevalent throughout the tropics, our data may indicate a significant global challenge to calculating global carbon fluxes, as selectively-logged forests now represent more than one third of all standing tropical humid forests worldwide.