Ecological sanitation (EcoSan) concepts, relying on an environmentally sound management of water, nutrient and energy fluxes, have been poorly characterized in literature and are widely ignored by public planning authorities, architects or engineers. A comparative life cycle assessment (LCA) of an EcoSan system at an office building and of conventional systems was carried out in order to provide practical data and information to (partially) fill this gap. Compared to conventional systems, EcoSan can reduce the contribution to ecosystem quality damage by more than 60%. EcoSan leads, however, to higher damages on resources and human health and higher impact on climate change. Key improvement possibilities and research needs related to these results are discussed throughout the paper. Ecological sanitation appears to be a promising alternative to small-scale wastewater treatment. At higher scales, low water consumption conventional systems are better performing and are not likely to be replaced by EcoSan systems in the short term. Standard conventional systems have very poor environmental performances and should be upgraded as far as possible.