Purpose: To evaluate the effect of a full-mouth disinfection protocol (FMD) on periodontal parameters, glycaemic control and subgingival microbiota of periodontal patients with type 1 and type 2 diabetes, as well as those without diabetes. Materials and Methods: This study included 33 patients with periodontitis. Eleven of them were type 1 diabetes patients, 11 were type 2 diabetes patients, and 11 were non-diabetics. At baseline and 3 months after the FMD, the periodontal parameters of each patient were recorded, samples of capillary blood for the chairside assessment of HbA1c were taken, and plaque samples from the two deepest periodontal pockets were collected to test for the presence of Aggregatibacter actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Tannerella forsythia (Tf) and Treponema denticola (Td). Results: Bleeding on probing (BOP), probing pocket depth (PPD), clinical attachment level (CAL) and glycated haemoglobin (HbA1c) decreased statistically significantly (p < 0.05) in all three groups 3 months after FMD. Only the
proportion of Pg in the control group decreased statistically significantly (p < 0.05), while the proportion of other
bacteria decreased or remained the same, whereby the differences were not statistically significant. Moreover, the
proportion of Aa in type 1 diabetics increased statistically significantly (p < 0.05). Conclusion: The FMD protocol improves periodontal parameters and glycaemic control of type 1 and type 2 diabetes
patients with periodontitis.