In the social debate about animal welfare we can identify three different views about how animals should be raised and how their welfare should be judged: (1) the view that animals should be raised under conditions that promote good biological functioning in the sense of health, growth and reproduction, (2) the view that animals should be raised in ways that minimise suffering and promote contentment, and (3) the view that animals should be allowed to lead relatively natural lives. When attempting to assess animal welfare, different scientists select different criteria, reflecting one or more of these value-dependent views. Even when ostensibly covering all three views, scientists may differ in what they treat as inherently important versus only instrumentally important, and their selection of variables may be further influenced by a desire to use measures that are scientifically respected and can be scored objectively. Value assumptions may also enter animal welfare assessment at the farm and group level (1) when empirical data provide insufficient guidance on important issues, (2) when we need to weigh conflicting interests of different animals, and (3) when we need to weigh conflicting evidence from different variables. Although value assumptions cannot be eliminated from animal welfare assessment, they can be made more explicit as the first step in creating animal welfare assessment tools. Different value assumptions could lead to different welfare assessment tools, each claiming validity within a given set of assumptions.