In the design of chemical/energy production systems, a major challenge is to identify the bottleneck issues and improve its sustainability effectively. Due to the multi-dimensional feature of sustainability, how to account for the impacts of various design factors and the cause-and-effect relationships can be very difficult. This paper will present a sustainability root cause analysis method based on the combination of Pareto Analysis and Fishbone diagram. The sustainability of the process is assessed incorporating economic, environmental, societal and efficiency concerns. This methodology is able to help the designers focus the attention on the most important fundamental causes, discover opportunities for sustainability improvement and provide critical guidance to design for sustainability. The efficacy of this methodology will be demonstrated through a case study on a biodiesel production technology. (C) 2011 Elsevier Ltd. All rights reserved.