Several studies have indicated that scientists are likely to have an outlook on both facts and values that are different to that of lay people in important ways. This is one significant reason it is currently believed that in order for scientists to exercise a reliable ethical reflection about their research it is necessary for them to engage in dialogue with other stakeholders. This paper reports on an exercise to encourage a group of scientists to reflect on ethical issues without the presence of external stakeholders. It reports on the use of a reflection process with scientists working in the area of animal disease genomics (mainly drawn from the EADGENE EC Network of Excellence). This reflection process was facilitated by using an ethical engagement framework, a modified version of the Ethical Matrix. As judged by two criteria, a qualitative assessment of the outcomes and the participants' own assessment of the process, this independent reflective exercise was deemed to be successful. The discussions demonstrated a high level of complexity and depth, with participants demonstrating a clear perception of uncertainties and the context in which their research operates. Reflection on stakeholder views and values appeared to be embedded within the discussions. The finding from this exercise seems to indicate that even without the involvement of the wider stakeholder community, valuable reflection and worthwhile discourse can be generated from ethical reflection processes involving only scienitific project partners. Hence, the previous assumption that direct stakeholder engagement is necessary for ethical reflection does not appear to hold true in all cases; however, other reasons for involving a broad group of stakeholders relating to governance and social accountability of science remain.