Insertion of fixed orthodontic appliances can induce an increase in oral biofilm and thereby cause inflammation of the periodontal tissues. The purpose of this study was to perform a longitudinal analysis of clinical and microbial parameters after insertion of lingual brackets. Bleeding on probing (BOP), plaque index (PI), and pocket probing depth (PPD) were measured in 10 adults (8 females and 2 males, aged 29.0 +/- 4.7 years) who received treatment with custom-made lingual appliances (Incognito/iBraces) before (T0) and 3 months after beginning of treatment (T1). No supportive dental prophylaxis was undertaken. In addition, a 16S rRNA-based polymerase chain reaction (PCR) method was used to detect Aggregatibacter actinomycetemcomitans (Aa) and Porphyromonas gingivalis (Pg) in the crevicular fluid. A Wilcoxon test was used to compare clinical parameters at the buccal (control) and lingual sites between T0 and T1. At T0, BOP was 12.4 +/- 8.2 per cent, PPD 2.1 +/- 0.3 mm, and PI 0.1 +/- 0.2 at the buccal sites and at T1 14.3 +/- 8.1 per cent, 2.1 +/- 0.2 mm and 0.1 +/- 0.2, respectively. At the lingual sites, BOP was 22.2 +/- 19.0 per cent, PPD 2.3 +/- 0.3 mm, and PI 0.1 +/- 0.2 at T0 and at T1 56.2 +/- 31.6 per cent, 2.9 +/- 0.3 mm, and 1.2 +/- 1.1, respectively. Differences between T0 and T1 were significant for clinical parameters only at the lingual sites. Aa was found in five patients at baseline and in four at T1, whereas Pg was found in one patient at T0 and in two at T1. Insertion of fixed lingual appliances without supportive dental prophylaxis induced a worsening of clinical parameters restricted to the lingual sites, whereas the relative prevalence of Aa and Pg remained unchanged.