Purpose To evaluate the caries status of the Cystic fibrosis (CF) children and adolescents with the comparation of some biochemical markers, secretory-immunoglobulin-A (sIgA), and antimicrobial peptides in the saliva. Methods In this cross-sectional descriptive study, the approval Ethics Board was obtained. Unstimulated saliva samples were collected from CF and healthy control children (non-CF) patients. Both groups underwent the same dental and periodontal evaluation scheme of the assessment. Human beta defensin (HBD1), human alpha defensin (HNP-1), cathelicidin (LL-37), sIgA in saliva were evaluated by enzyme-linked immunoassay method. A general biochemical analysis was performed. Statistical analysis was performed by using Statistical Package for the Social Sciences Version 20.0 (SPSS Inc.). Results A total of 21 (9 male, 12 female) CF and 23 (11 male, 12 female) control patients were participated with the mean age of 10.17 +/- 3.38 and 9.52 +/- 2.15 years, respectively. In control children, DMFT/S (decayed-missing-filled-tooth/surface-in-permanent-dentition), dmft/s (decayed-missing-filled-tooth/surface-in-primary-dentition) values were higher; DT (decayed-tooth in permanent dentition), ft (filled-tooth in primary dentition) and plaque index values were statistically significantly higher (p = 0.042, p = 0.005, p = 0.038, respectively) than CF patients. Bicarbonate was higher in control group; sodium, chloride, and total protein were higher in CF group; magnesium, calcium and phosphate levels were similar in each group (p > 0.05). Alpha and beta defensin-1 levels in control group was statistically significantly higher (p = 0.037 and p = 0.020, respectively), while LL37 and sIgA were not statistically significantly higher (p > 0.05) than CF group. Conclusions Children with CF had lower caries in permanent teeth, filling in primary teeth, and an altered salivary biomarker profile, especially in HNB1, HNP1. Therefore, it is important to conduct periodic oral-dental controls among CF patients during their childhood.