We developed a whole-canopy CO(2) exchange simulation model to study effects of pruning on the carbon balance of trees. Model inputs include global short-wave radiation, photosynthetic photon flux density (PFD), air temperature, time series of the development of canopy diameter, height and total leaf area during the simulation period and local geographical and atmospheric parameters. Canopy structure is derived stochastically from the time series of canopy development and growth functions of individual phytoelements. The PFD incident on a phytoelement is computed from the average gap frequency of the canopy and the binary random probability of sunflecks on the phytoelement. Instantaneous CO(2) assimilation rate of each phytoelement is computed from PFD and phytoelement age. Assimilation rates are integrated over space and time to estimate whole-canopy CO(2) assimilation. The model was used to study carbon balance in five sources of the leguminous agroforestry tree Erythrina poeppigiana (Walpers) O.F. Cook during two 6-month pruning intervals. The canopy description appeared to be realistic. According to the simulations, cumulative assimilation did not provide enough carbon for tree growth until two months after pruning, indicating dependence of tree growth on reserve carbohydrates. The two most productive sources, which had the most open canopies, were the most dependent on reserve carbohydrates after pruning.