OBJECTIVES: To estimate the cost of PET/CT procedure with 18FDG as its radiotracer from the perspective of a Brazilian public provider of health services, in order to support economic evaluation studies about the technology. METHODS: The micro-costing technique was used, and all inputs consumed in the activities involved with the procedure have been identified, measured and valuated. This included capital costs, human resources, radiopharmaceutical 18FDG purchases, administrative costs and others. Data for cost estimates were collected from the observation of 85 exams at the Brazilian National Cancer Institute (INCA) from March to June 2012. The reference case considered adult cancer patients, daily production of 5 exams using one FDG dose per patient. INCA employees, because of their research activities, receive differentiated wages (from Science and Technology –S&T- career), than the usual employees of federal public hospitals where new PET/CTs might be installed receive (from Ministry of Health -MoH). So, to avoid biases, two cost estimates were carried out considering different wage modalities (MoH and S&T career). Also, sensitivity analysis examined elements that might impact on the costs in public health institutions. RESULTS: The average costs of the procedure for the reference case were US$1612.23 for Science and Technology career’s wages, and US$1498.05 for Ministry of Health’s wages. When a scenario of full capacity of exams was considered (10 procedures/day), average costs were significantly smaller: US$1023.47 for S&T and US$966.38 for MoH. The largest factors of impact on costs were daily volume of procedures, human resources, and price of 18FDG. CONCLUSIONS: Despite its growing applicability in diagnosis, the technology is still complex and aggregate high costs on health system. This is the first study which estimates cost of PET/CT technic in Brazil. PET procedure is in the pipeline to be reimbursed and this study could contribute to the reference value construction.