Abstract Aim The aim was to investigate the salivary detection frequencies and quantities of caries‐associated bacteria from patients with orthodontic brackets. Methods Patients wearing orthodontic brackets (n = 40, mean age = 26 years) and healthy controls without brackets (n = 40, mean age = 17 years) were enrolled in the study. Saliva samples from each patient was collected. After DNA purification, target species comprising streptococci and a Lactobacillus species were detected and quantified from the samples using polymerase chain reaction (PCR) and real‐time quantitative PCR. Results Detection frequencies did not differ between the orthodontic patients and the control subjects for any target species except for Streptococcus sobrinus, which showed significantly lower detection rates in orthodontic patients (p < .05). Lactobacillus casei and Streptococcus gordonii were found at the highest detection frequencies with both species being detected in 38 (95%) of the saliva samples of orthodontic patients. Similarly, L. casei and Streptococcus salivarius were the species with highest detection frequencies (35, 87.5%) in the control subjects. Real‐time PCR revealed that Streptococcus mutans and S. salivarius quantities were significantly higher in orthodontic patients than in the control subjects (p < .05). Conclusions Application of orthodontic brackets for 12 months leads to increased salivary levels of cariogenic bacteria and may serve as a potential risk factor for caries initiation.