Background and objectives: It is known that orthodontic therapy might alter various oral and salivary findings, especially if patients do not impose better oral hygiene practices at home as well as certain dietary habit changes. Therefore, it is expected that certain bacterial rods would be more frequent in these patients, especially when correlated to the white spot lesions development. Furthermore, changes in the pH of the saliva and plaque is expected as it was suggested from the previous finding of various authors. This might result in the worsening of the DMFT index. At present there are no recorded longitudinal clinical trials monitoring the changes of microbiological and physiological parameters of saliva in patients with orthodontic brackets of various designs and materials. Materials and methods: Each study group consisted of 21 patients with different type of fixed orthodontic appliance - aesthetic conventional and aesthetic self-ligating brackets, metal conventional and metal self-ligating brackets. For all patients the following was determined: pH of plaque, presence of initial carious lesions (by means of Diagnodent), salivary levels of electrolytes (titanium, nickel, copper, zinc, chromium and cobalt) by use of inductively coupled plasma mass spectrometry, the number and species of the bacteria present (by means of mass spectrometry), the DMFT index, dietary habits and oral hygiene by use of questionnaire with eight questions. Statistical analysis was performed by use of Kolmogorov Smirnov test in order to determine normality of the data distribution. As the data were normally distributed, T-test for dependent samples was applied for the measurment immediately after bracket installment and six months later. In order to determine differences between boys and girls as well as differences between various bracket types, T-test for independent samples was used. P-values lower than 0.05 (p < 0.05) were considered as statistically significant. Results: Overall, 28,57% of teeth showed deterioration in white spot finding and the total of 24 patients developed a new white spot lesion. White spot lesion at first measurement were noticed on the 17.86 % of the teeth, while on the second measurment they were present on 46.43 % teeth. There were no significant differences in the occurrence of white spot lesions regarding the features of the brackets. There was a significant difference in pH of the plaque after the brackets were inserted no matter which ones. On the first measurment, pH of the plaque was 6.0, whereas on the second measurment pH of the plaque was 6.25, which means that it was more alkaline. It seems that the patients implemented better oral hygiene measures when they got orthodontic appliances. Plaque index deteriorated after the brackets were inserted, however the difference did not reach statistical significance, regardless of the type of the bracket. The DMFT index increased after insertion of the fixed orthodontic appliance, regardless of the bracket type. Salivary flow rate increased after the brackets were inserted, expecially in patients with aesthetic conventional brackets. Salivary concentrations of titanium were significantly higher after six months of treatment. Salivary titanium levels were higher in patients with metallic conventional brackets when compared to the ones with metallic self-ligating brackets. Salivary chromium and zinc concentrations were significantly higher at the first measurment when compared to the second one. Bacterial composition of the plaque determined by use of mass spectrometry showed continuous presence of the following bacteria: Capnocytophaga, Veilonella, Streptococcus parasanguinis and Streptococcus mutans. New bacteria which appeared together with deterioration of white spot lesions was Campylobacter. Significant difference was observed in the usage of interdental brushes before the treatment and six months after the insertion of orthodontic appliance. The initial measurement and the second measurement found no significant differences regarding food consumption habits (meals, snacks, sweets, sweetened drinks, chewing gums) and oral hygiene practices (brushing and flossing) regardless of the bracket type. Conclusions: Orthodontic treatment leads to an increased tendency to formation of white spot lesions and an increase in the DMFT index, salivary flow rate and pH of the plaque although plaque index do not change significantly. It seems that the participants did not change their eating habits, only increased use of interdental brushes was noticed. It seems that bracket type does not influence any of the examined parameters except salivary titanium levels and salivary flow rate.