Many countries are undertaking widespread structural change of their health sectors. There is mounting concern that priority-setting mechanisms used in planning the reforms are not suited to recognizing or taking account of the needs and priorities of sexual and reproductive health (SRH) services. The main aim of this research was to assess the sensitivity of the priority-setting tools and mechanisms used in the development of the health sector reforms in Ghana, to the needs and priorities of SRH services, and to consider how priority-setting mechanisms could be improved. We conclude that priority-setting tools in Ghana's reform process were rudimentary, and SRH donors and advocates were little involved. While it is tempting for a strong programme like Ghana's SRH programme to remain independent, we argue that closer involvement in system-wide reforms is a preferable long-term objective. Clearly, SRH priorities need safeguarding within a systems approach and we suggest a number of ways in which this can be achieved. Most importantly, the SRH community, in collaboration with the wider development community, needs to challenge current priority-setting mechanisms and the long-held view that traditional disease-ranking and cost-effectiveness measures are necessarily the best, most accurate way to measure health priorities. Traditional priority-setting tools do not adequately reflect the long-term benefits of preventive interventions such as family planning, and are therefore not an adequate reflection of holistic health sector planning needs. In response to this, there needs to be greater commitment from the international development and research communities to: (1) support collaboration between economists and reproductive health specialists to develop better measures for the effectiveness and impact of SRH services; and (2) in the interim, accept proxies for priority-setting which may include small-scale, qualitative research data combined with priorities identified by SRH specialists. To achieve this, the priority-setting processes need to become more inclusive and SRH specialists need to be proactive in their engagement with health sector decision-makers.