Appropriately identifying and representing stakeholders' interests and viewpoints in evaluations of health information technology (health IT) is a critical part of ensuring continued progress and innovation in eHealth. This contribution therefore seeks to clarify the principles of stakeholder analysis in an eHealth context. We describe this with reference to a mixed methods national evaluation of ePrescribing systems in English hospitals. We use this evaluation to exemplify the engagement and analytical tools required to ensure a detailed understanding of the issues, challenges and lessons learnt across stakeholder groups. We conclude that this type of approach may support the robustness of evaluations of health IT as well as their longer term impact on innovation in the field.