BACKGROUND:Accounting for carbon gains and losses in young-growth forests is a key part of carbon assessments. A common silvicultural practice in young forests is thinning to increase the growth rate of residual trees. However, the effect of thinning on total stand carbon stock in these stands is uncertain. In this study we used data from 284 long-term growth and yield plots to quantify the carbon stock in unthinned and thinned young growth conifer stands in the Alaskan coastal temperate rainforest. We estimated carbon stocks and carbon accretion rates for three thinning treatments (basal area removal of 47, 60, and 73 %) and a no-thin treatment across a range of productivity classes and ages. We also accounted for the carbon content in dead trees to quantify the influence of both thinning and natural mortality in unthinned stands. RESULTS:The total tree carbon stock in naturally-regenerating unthinned young-growth forests estimated as the asymptote of the accretion curve was 484 (±26) Mg C ha-1 for live and dead trees and 398 (±20) Mg C ha-1 for live trees only. The total tree carbon stock was reduced by 16, 26, and 39 % at stand age 40 y across the increasing range of basal area removal. Modeled linear carbon accretion rates of stands 40 years after treatment were not markedly different with increasing intensity of basal area removal from reference stand values of 4.45 Mg C ha-1 year-1to treatment stand values of 5.01, 4.83, and 4.68 Mg C ha-1 year-1 respectively. However, the carbon stock reduction in thinned stands compared to the stock of carbon in the unthinned plots was maintained over the entire 100 year period of observation. CONCLUSIONS:Thinning treatments in regenerating forest stands reduce forest carbon stocks, while carbon accretion rates recovered and were similar to unthinned stands. However, that the reduction of carbon stocks in thinned stands persisted for a century indicate that the unthinned treatment option is the optimal choice for short-term carbon sequestration. Other ecologically beneficial results of thinning may override the loss of carbon due to treatment. Our model estimates can be used to calculate regional carbon losses, alleviating uncertainty in calculating the carbon cost of the treatments.