Background: Saliva and sweat are modified by cystic fibrosis (CF). In both cases the chloride and sodium ion concentrations for healthy subjects and CF patients differ, this representing a possible alternative tool for CF diagnosis. In this context, the aim of this study was to compare the concentrations of these ions in saliva samples taken from CF patients and healthy subjects. Methods: A case-control study was carried out at a university CF center, in which the saliva samples were analyzed on an ABL 835 Radiometer (R) to determine the ion concentration. Results: For the CF patients (n = 80) the values for the biochemical parameters of chloride, potassium and sodium ion concentration were higher (p < 0.009) and the volume and pH of the saliva were lower than in the case of healthy subjects (p < 0.009). For the healthy subjects group (n = 84) versus CF patients, according to the ROC curve, the values for sodium were: cutoff: 13.5 mmol/L, sensitivity: 73.4%, specificity: 70.6%; and for chloride: cutoff: 20 mmol/L, sensitivity: 68.1%, specificity: 72.9%. Conclusions: The chloride and sodium concentrations in the saliva samples were higher for CF patients in comparison with healthy subjects. Thus, saliva as a tool for CF diagnosis can be considered a new challenge, and a population study including patients in all age classes needs to be performed, in different countries over the world, to extend the database to include a broad spectrum of information in order to identify normal ion concentration ranges for CF patients according to age, genotype and environment.8