Changes in the composition of saliva can be related to different physiological processes and various oral diseases. Examination of saliva as a diagnostic environment for various biomarkers is a modern method that has been used in dental medicine since last century. Aim of the study was in vivo investigation of topical fluorides and prophylactic remineralizing procedures’ influence on the end products of fat and protein metabolism in the saliva. The results showed that aggressive carbohydrate attacks or stimulation of carbohydrate cariogenic metabolism in the dental plaque did not affect the metabolic profile of the fatty and amino acids in the saliva. Topical fluoride application during the course of oral prophylactic procedures in children also did not change the concentration of the fatty and amino acids.