The Walker and Harremoës (W&H) uncertainty framework is a tool to systematically identify scientific uncertainty. We applied the W&H uncertainty framework to elicit scientists' judgements of potential sources of uncertainty associated with the use of DNA vaccination in aquaculture. DNA vaccination is considered a promising solution to combat pathological fish diseases. There is, however, lack of knowledge regarding its ecological and social implications. Our findings indicate that scientists are open and aware of a number of uncertainties associated with DNA vaccination e.g. with regard to immune response, degradation and distribution of the DNA plasmid after injection and environmental release, and consider most of these uncertainties to be adequately reduced through more research. We proceed to discuss our experience of using the W&H uncertainty framework. Some challenges related to the application of the framework were recognised. This was especially related to the respondents' unfamiliarity with the concepts used and their lack of experience in discussing qualitative aspects of uncertainties. As we see it, the W&H framework should be considered as a useful tool to stimulate reflection on uncertainty and an important first step in a more extensive process of including and properly dealing with uncertainties in science and policymaking.