Oral fluid is a valuable substrate for assessing dental health and other aspects of physical status. New methods for early diagnosis and prognosis of dental diseases on the basis of oral fluid composition are in constant demand. Excessive fluoride concentrations, often oversighted by dental therapists, negatively affect organs and tissues of the oral cavity. This study aimed at development and approbation of a method for reliable measurement of fluoride ions in oral fluid by capillary electrophoresis to be used in patients with dental diseases. The fluoride ion concentrations were measured in health (2.16 ± 0.48 mg/L), in isolated acute pericoronitis (15.2 ± 2.7 mg/L) and in acute pericoronitis combined to multiple caries (18.9 ± 4.2 mg/L). By post-operative day 3, fluoride levels in the group with isolated acute pericoronitis dropped to normal values (2.28 ± 0.52 mg/L), whereas in the group with acute pericoronitis combined to multiple caries fluoride levels remained high (8.7 ± 1.9 mg/L; р < 0.0001). The developed protocol is efficient for studying fluoride ion concentrations in isolated and combined dental diseases.