We determined the short-term direct and long-term indirect effects of CO2 on apparent dark respiration (CO2 efflux in the dark) in ponderosa pine (Pinus ponderosa Dougl. ex Laws.) seedlings grown in 35 or 70 Pa CO2 partial pressure for 163 days in naturally lit, controlled-environment chambers. Two soil N treatments (7 and 107 ppm total N, low-N and high-N treatments, respectively) were imposed by watering half the plants every 2 weeks with 15/15/18 fertilizer (N,P,K) and the other half with demineralized water. Direct effects of ambient CO2 partial pressure on apparent dark respiration were measured during short-term manipulations (from minutes to hours) of the CO2 environment surrounding the aboveground portion of individual seedlings. Short-term increases in the ambient CO2 partial pressure consistently resulted in significant decreases in CO2 efflux of seedling in all treatments. Efflux of CO2 decreased by 3 to 13% when measurement CO2 partial pressure was increased from 35 to 70 Pa, and by 8 to 46% over the entire measurement range from 0 to 100 Pa. No significant interactions between the indirect effects of growth CO2 partial pressure and the direct effects of the measurement CO2 partial pressure were found. Seedlings grown in the high-N treatment were significantly less sensitive to short-term changes in CO2 partial pressures than seedlings grown in the low-N treatment. Apparent respiration tended to decrease in seedlings grown in elevated CO2, but the decrease was not significant. Nitrogen had a large effect on CO2 efflux, increasing apparent respiration more than twofold on both a leaf area and a leaf or shoot mass basis. Both the direct and indirect effects of elevated CO2 were correlated with changes in the C/N ratio. A model of cumulative CO2 efflux for a 160-day period demonstrated that, despite a 49% increase in total plant biomass, seedlings grown in the high-N + high-CO2 treatment lost only 2% more carbon than seedlings grown in the high-N + low-CO2 treatment, suggesting increased carbon use efficiency in plants grown in elevated CO2. We conclude that small changes in instantaneous CO2 efflux, such as those observed in ponderosa pine seedlings, could scale to large changes in carbon sequestration.