Complex interventions, involving interlinked packages of care, challenge the application of current methods of economic evaluation that focus on measuring only health gain. Complex interventions may be problematic on two levels. The complexity means the intervention may not fit into one of the current appraisal systems, and/or maximising health is not the only objective. This paper discusses the implications of a programme of work that focused on clinical genetics services, as an example of a complex intervention, and aimed to identify the following: the attributes that comprise both health and non-health aspects of benefits and whether it is possible to evaluate such an intervention using current National Institute for Health and Clinical Excellence appraisal processes. Genetic services and tests are a good example of a complex intervention and have broader objectives than just health gain, which may usefully be measured using the concept related to capability, which we have called ‘empowerment’. Further methodological work is required to identify the trade-off between non-health (empowerment) and health benefits for other complex interventions. We do not advocate a move away from QALY maximisation but do suggest that there is a need for a more considered approach that can take account of the perceived value for non-health attributes for some complex interventions. Copyright © 2012 John Wiley & Sons, Ltd.