The estimation of whole canopy carbon assimilation rate using the relationship between daily net CO2 assimilation rate (An) and daily incident photosynthetically active radiation (PAR) for individual leaves within the canopy has been considered an alternative to whole canopy gas exchange measurements. This relationship has been reported as being linear, but it has been explored only between the end of active shoot growth and harvest and in few species. Apple (Malus domestica) trees were used to study the seasonal changes in the relationship between daily An and incident PAR in individual leaves during the growing season of 2007 and this was done for pear (Pyrus communis) trees in 2008. Fifty leaves exposed to different light environments within the canopy of a given tree were selected. For each leaf seven times a day incident PAR and An was measured. Daily incident PAR and An was estimated by integrating instantaneous values. The relationship between daily An and daily incident PAR within the canopy had different patterns depending on the time of the season. It was always curvilinear early and late in the season, but tended to be more linear between the end of active shoot and harvest (mid-season). The initial slope and curvature of the relationship changed during the season and both were significantly related to daily PAR above the canopy.Whole canopy net carbon exchange rate was estimated considering canopy intercepted PAR and the relationship between daily An and incident PAR in individual leaves. The values were similar to those reported in the literature during mid-season. Estimated whole canopy net carbon exchange rate varied substantially after harvest, depending on whether a linear or curvilinear response of daily An to PAR for individual leaves within the canopy was considered. We showed that apple and pear whole canopy net carbon exchange rate can be estimated during mid-season, which is the most relevant phase for tree fruit production, using the following parameters: photosynthetic rate of well exposed leaves, daily pattern of incident photosynthetically active radiation (PAR), daily integral of PAR intercepted by the canopy and leaf area.