Rationale, aims and objectives Clinical guidelines are tools that systematize scientific evidence and help to achieve proper care. Several difficulties are reported regarding the effective use, such as the shortcomings in the level of knowledge and attitudes by the professionals, the service structure and the preferences appointed by patients. An analysis of these difficulties was the objective of this study in the context of government Neonatal Intensive Care Units (NICU) in Brazil. Method A semi-structured survey was carried out with 53 managers (medical and nursing) of the 15 NICU in a convenient sample of two groups of government units in Brazil. The managers chose their answers from a list of difficulties to implement the guidelines based on the analytical model of Cabana and graded the difficulties found on a 5-point scale with no reference to quality. Results Respondents have reported several difficulties with the following priority: lack of professionals to provide care, being perceived as more critical within the nursing and physiotherapy crews, minor participation of professionals in the discussion process and inadequate infrastructure. The lack of acquaintance with the guidelines by the professionals has been reported by few of the surveyed. Conclusion These findings show some common ground to literature pointing the importance of adequate infrastructure. Managers showed a low valuation of both the level of knowledge and the professionals’ adhesion to the guidelines.