The authors comment on the need to translate into operational instructions the principles and concepts that guided the VIII National Conference in Health convened by the Ministry of Health of Brazil, to make possible the reorganization of the health system. It is emphasized that the model for organizing the primary health care proposed by the Integrated Health Actions (AIS) and assumed by the Unified and Decentralized Health System (SUDS), implies a progressive redefinition of the especial programs in public health. The authors describe the efforts of the Health Department of the State of Bahia (SESAB) during the implementation of the SUDS to make compatible the operations of the especial programs with the primary health care model. The resistance observed to the new directions and the attempts to overcome it, are analysed, as well as the transition (unfinished) to the proposed health care model. It is proposed an alternative model for the internal organization of health care units which take into consideration the emerging demands and also the available offers to deal with priority health problems. As conclusion, the authors state that some special programs can continue to be developed within a unified and decentralized health care model, due to their technical and scientifical value, since these programs are adequated to the political principles of the Health System Reform in Brazil.
