Insertion of fixed orthodontic appliances induces increased biofilm formation caused by a higher number of plaque-retentive sites. The purpose of the study was to perform a quantitative analysis of supra- and subgingival long-term biofilm formation on orthodontic bands. Ten patients (five females and five males, aged 18.3 +/- 5.4 years) who had received therapy with fixed orthodontic appliances for 24 +/- 9 months were enrolled in the study. Biofilm formation on 28 orthodontic bands was analyzed quantitatively with the Rutherford backscattering detection method, a scanning electron microscopy technique. The biofilm formation for the supra- and subgingival surfaces was calculated from the grey values. Statistical analysis was performed with a mixed model with the patient as the random factor. A P-value < 0.05 was considered significant. A biofilm was found on 16.1 +/- 9.2 per cent of supragingival surfaces and on 3.6 +/- 4.4 per cent of subgingival surfaces. Differences in biofilm formation in supra- and subgingival surfaces were statistically significant (P < 0.05) and formed a distinct demarcation line. Despite the presence of supragingival biofilm, no mature subgingival biofilm was found on the tested orthodontic bands.