Background In cystic fibrosis (CF) one of the most important indicators of the quality of care is the expected life years. Median life expectancy increased to more than forty years in Western European countries. On the contrary, in Hungary it remained only 16 years as determined in 2013. Objectives We aimed to assess if suboptimal use of medication recommended by recent international guidelines for CF care may contribute to the limited life expectancy of CF patients in Hungary. Therefore we evaluated the use of common inhaled and oral medications in our nationwide database. Methods Pharmacy refill records of dornase alpha and pancreas enzyme replacement therapy (PERT) were evaluated based on the data of the Hungarian Health Insurance Fund between 2010 and 2012. Expected drug consumption was calculated by CF guidelines based on annual patient number and compared to the actual records on pharmacy refill. Results Adherence ranged from 17.4% to 18.6% for dornase alpha during the three-year-period. 5–7% of the patients used dornase alpha under the age of five. In this patient group, however, there is no evidence for its use. Only every fourth adult patient used PERT in the period of the study. Conclusions The results demonstrated poor treatment adherence to both oral and inhalation therapies. Causes of this inadequate adherence may be explained not only by patients' attitudes, but also by the insufficient number of prescriptions suggesting suboptimal care. The lack of evidence-based use of dornase alpha highlighted the importance to improve daily CF care. More rigorous treatment protocols and regular audit could lead to optimal CF care hereby better life expectancy.