Whereas life cycle assessment (LCA) is more and more used for assessing the environmental load of waste management systems and of biomass production and valorization systems, various scientific issues are still to be dealt with. The purpose of this paper is to enlighten these scientific issues and to describe the current attempt to overcome them. The method used has been to go through the steps of the LCA standardized framework (ISO 14040) and to outline at each step the points that could be improved and still deserve research efforts. The various identified issues are: in step 1 (goal and scope), the choice of attributional/consequential modelling, the difficult choice of the functional unit due to the highly multi-functional nature of such systems, the allocation choices and the need for spatial differentiation; in step 2 (inventory), the thorny issue of modelling such complex systems and properly estimating field emissions; in step 3 (impact assessment), the lack of appropriate impacts (such as odours) in current LCA impact categories; in step 4 (interpretation and use), research efforts are needed to understand and facilitate the way actors take over and use LCA multi-criteria results. A transversal issue, i.e. uncertainty characterization and reduction, is also analyzed. These various scientific bottlenecks are currently under study; some are handled by this "Waste and Biomass Valorization" special topic, which includes a selection of papers presented in 2011 at the Ecotech&Tools conference (Montpellier, France).