A central aim of animal welfare science is to be able to compare the effects of different ways of keeping, managing or treating animals based on welfare indicators. A system to aggregate the different indicators is therefore needed. However, developing such a system gives rise to serious challenges. Here, we focus specifically on the ethical aspects of this problem, taking as our starting point the ambitious efforts to set up an aggregation system within the project Welfare Quality® (WQ). We first consider the distinction between intra- and inter-individual aggregation. These are of a very different nature, with inter-individual aggregation potentially giving rise to much more serious ethical disagreement than intra-individual aggregation. Secondly, we look at the idea of aggregation with a focus on how to compare different levels and sorts of welfare problems. Here, we conclude that animal welfare should not be understood as a simple additive function of negative or positive states. We also conclude that there are significant differences in the perceived validity and importance of different kinds of welfare indicators. Based on this, we evaluate how aggregation is undertaken in WQ. The main conclusion of this discussion is that the WQ system lacks transparency, allows important problems to be covered up, and has severe shortcomings when it comes to the role assigned to experts. These shortcomings may have serious consequences for animal welfare when the WQ scheme at farm or group level is applied. We conclude by suggesting ways to overcome some of these shortcomings.