Sunflower (Helianthus annuus L.) and rapeseed (Brassica napus L.) are considered as the most suitable crops for biodiesel production in the Mediterranean basin. Soybean (Glycine max L.) could also be used, under certain conditions. In Greece, the farming practice adopted in each region varies significantly, leading to significant differences in the levels of emitted greenhouse gases (GHG). Greenhouse gas emissions were estimated during the cultivation phase as grams of carbon dioxide equivalents (g CO2e) per megajoule (MJ), followed by emission savings (%) estimation when fossil fuels are replaced by biodiesel. Crop and region comparisons provided important information towards promoting sustainability. Overall, sunflower demonstrated the lowest average emissions, 53·8 g CO2e/MJ, followed by rapeseed and soybean. Furthermore, rapeseed achieved the lowest emission saving level required by European legislation in most cases studied, with an average value of 37%. Irrigation and nitrogen fertilization were the operations mostly contributing to the total quantity of GHG emissions. More specifically, the highest GHG emissions were found for soybean irrigation (34%) and rapeseed nitrogen fertilization (68%).