OBJECTIVES: To compare costs of specialized units of complementary and alternative medicine (CAM) in northeastern region in Brazil, inserted in Sistema Único de Saúde (SUS, in English, Unified Health System). METHODS: Selected units were public, specialized in CAM and from close states. However, Unit A is older, smaller in dimension, localized in a rented house adapted, attends during the week in business hours, and SUS patients have access majorly through medical recommendation. Unit B is newer, bigger, built for its finality, open in week days from morning until early evening and Saturdays mornings, and most patients arrive by spontaneous demand. Costs data were collected through secondary information (local government sources), and resources data by direct observation. After valuation, resources items were organized following the absorption costing method, and divided into costing centers: productive, administrative and auxiliary. RESULTS: Yearly cost for 2014 from Unit A was estimated at US$561,996.02, of which 93,4% were direct costs. Unit B was estimated at US$621,581.68, of this amount, 79.69% were classified as direct costs. Productive costing center represented 64.5% and 67.69% for Units A and B, respectively. When compared to informed production (individual or group sessions), average cost per session was US$45.74 for Unit A and US$58.15 for Unit B. CONCLUSIONS: In total, Unit A costs are similar to Unit B, although the later offer better quality in terms of infrastructure, number of professionals and variety of services offered. Therefore, it is comprehensible the larger expense in Unit B with indirect costs. Cost per session are equivalent to those found in medium complexity biomedical services available in SUS. Currently, there is no similar study in Brazil to compare results, and further studies are needed to compare costs of other public MAC specialized centers in Brazil.