The aim of the study was to assess the influence of fixed orthodontic appliance on Streptococcus (S.) mutans and S. sobrinus counts in orthodontic patients with regard to their previous caries experience (Decayed, Missing and Filled Teeth (DMFT) index) during the first 12 weeks of orthodontic treatment. Twenty-two patients that satisfied inclusion criteria (healthy systemic and periodontal condition, avoidance of antibiotic therapy and antiseptic mouthwashes in the past three months) were included. All clinical measurements took place prior to and 12 weeks after fixed orthodontic appliance placement, in the following order: 1) stimulated saliva flow (SS); 2) Simplified Oral Hygiene Index (OHI-S); and 3) DMFT. The method of polymerase chain reaction (PCR) was used to detect the presence of S. mutans and S. sobrinus at T1 and T2. T-test showed significant increase in DMFT index and SS between T1 and T2. Results also indicated significant improvement in OHI-S index. By use of the PCR method, S. mutans was detected in two patients at T1. At T2, two more patients had S. mutans, but the increase was not statistically significant. Using the same method, S. sobrinus was detected only in two patients at T2. In conclusion, fixed orthodontic appliances did not induce statistically significant changes in caries microflora even in the presence of enhanced oral hygiene habits.