Energy crops are expected to greatly develop in a very short-term bringing to significant social and environmental benefits. Nevertheless, a significant number of studies report from very positive to negative environmental implications from growing and processing energy crops, thus great uncertainty still remains on this argument. The present study focused on the cradle-to-grave impact assessments of alternative scenarios including annual and perennial energy crops for electricity/heat or first and second generation transport fuels, giving special emphasis to agricultural practices which are frequently surprisingly neglected in Life Cycle Assessment studies despite a not secondary relevance on final outcomes. The results show that cradle-to-farm gate impacts, i.e. including the upstream processes, may account for up to 95% of total impacts, with dominant effects on marine water ecotoxicity. Therefore, by increasing the sustainability of crop management through minimizing agronomic inputs, or with a complementary use of crop resides, can be expected to significantly improve the overall sustainability of bioenergy chains, as well as the competitiveness against fossil counterparts. Once again, perennial crops resulted in substantially higher environmental benefits than annual crops. It is shown that significant amount of emitted CO(2) can be avoided through converting arable lands into perennial grasslands. Besides, due to lack of certain data, soil carbon storage was not included in the calculations, while N(2)O emission was considered as omitted variable bias (1% of N-fertilization). Therefore, especially for perennial grasses, CO(2) savings were reasonably higher that those estimated in the present study. For first generation biodiesel, sunflower showed a lower energy-based impacts than rapeseed, while wheat should be preferred over maize for first generation bioethanol given its lower land-based impacts. For second generation biofuels and thermo-chemical energy, switchgrass provided the highest environmental benefits. With regard to bioenergy systems, first generation biodiesel was less impacting than first generation bioethanol; bioelectricity was less impacting than first generation biofuels and second generation bioethanol by thermo-chemical hydrolysis, but highly impacting than Biomass-to-Liquid biodiesel and second generation bioethanol through enzymatic hydrolysis. (C) 2011 Elsevier Ltd. All rights reserved.