BackgroundIn Tanzania, decentralisation processes and reforms in the health sector aimed at improving planning and accountability in the sector. As a result, districts were given authority to undertake local planning and set priorities as well as allocate resources fairly to promote the health of a population with varied needs. Nevertheless, priority setting in the health care service has remained a challenge. The study assessed the priority setting processes in the planning of the prevention of mother to child transmission of HIV (PMTCT) programme at the district level in Tanzania.MethodsThis qualitative study was conducted in Mbarali district, south-western Tanzania. The study applied in-depth interviews and focus group discussions in the data collection. Informants included members of the Council Health Management Team, regional PMTCT managers and health facility providers.ResultsTwo plans were reported where PMTCT activities could be accommodated; the Comprehensive Council Health Plan and the Regional PMTCT Plan that was donor funded. As donors had their own globally defined priorities, it proved difficult for district and regional managers to accommodate locally defined PMTCT priorities in these plans. As a result few of these were funded. Guidelines and main priority areas of the Ministry of Health and Social Welfare (MoHSW) also impacted on the ability of the districts and regions to act, undermining the effectiveness of the decentralisation policy in the health sector.ConclusionThe challenges in the priority setting processes revealed within the PMTCT initiative indicate substantial weaknesses in implementing the Tanzania decentralisation policy. There is an urgent need to revive the strategies and aims of the decentralisation policy at all levels of the health care system with a view to improving health service delivery.