Jatropha shrubs grow tall if left non-pruned. Pruning helps to keep the height within harvestable distances. Since, Jatropha flowers are borne on leaf axils of new growth in the season, pruning is supposed to increase fruiting because of formation of more number of lateral branches due to suppression of apical dominance. However, results of exploratory studies revealed drastic reduction of fruit yield after pruning. The results assume importance because lesser yield obtained owing to pruning would be uneconomical, both to the growers on account of diminished returns and to the biodiesel industry on account of being idle because of short seed supply. In this report, we found that paclobutrazol (PBZ) application induced flowering and fruiting in pruned shrubs and partially made up for the yield loss, besides keeping a lower plant height. With PBZ application, the yield reduction compared to non-pruned shrubs was limited to 67%, while 98% reduction in capsule yield was observed in untreated pruned shrubs. Paclobutrazol application along with pruning altered the morphology and vegetative growth of Jatropha, producing shrubs with smaller leaves with enhanced chlorophyll and nitrogen content and increased photosynthetic rate. It was found that though more secondary branching is induced in pruned plants, lesser tertiary branches on them results in no additional advantage with respect to total branches. However, the important objective of keeping the branches nearer to the ground is met. The effect of the treatments in terms of energy output from oil, de-oiled cake, capsule shell/husk has also been reported. (C) 2010 Elsevier Ltd. All rights reserved.