Antimicrobial Photodynamic Therapy (aPDT) for periodontal disease (PD) treatment has been studied for more than three decades, but there is no consensus among researchers about its role on PD control. PD is an oral infection linked with a variate of systemic diseases affecting mainly immunocompromised and elderly patients. The aim of this study is to evaluate aPDT for PD control and to analyze the periodontal microbiological profile regarding healthcare-associated infections (HAI). Six patients were enrolled in this study and the microbiological profile of 36 sites were evaluated in different moments: initial, after scaling and root planing, after aPDT and one-week post-treatment. aPDT was performed with 100μM water solution of methylene blue (MB), and a diode laser (100mW, 660nm, 90s per point, 9J). After periodontal therapy the pockets were irrigated with hydrogen peroxide (3%), washed with water, and MB was applied when no bleeding was detected. To collect the periodontal pocket content, a sterilized paper point was placed inside the pocket for 30s. The material was transferred to a vial with transport culture medium and sent to a microbiological facility to be analyzed blindly. The results showed the presence of pathogens linked with HAI as Acinetobacter baumannii, Candida albicans e Serratia marcescens immediately after therapy, but one week after treatment, none of them were detected and the periodontal index of all patients improved. This preliminary result point out that aPDT may not only improve periodontal clinical conditions, but also can diminish the systemic-health threat represented by this disease.