The aim of this work was to investigate the long-term effects of a single application of a water-cooled pulsed neodymium yttrium aluminium garnet (Nd:YAG) laser, in combination with scaling and root planing (SRP) for the treatment of periodontal inflammation. Twenty-two patients were included in this split-mouth single blind randomized controlled clinical trial. The parameters of the air and water-cooled Nd:YAG laser were: 4 W, 80 mJ/pulse, 50 Hz and a pulse width of 350 μs. The "test side" was treated with a single application of Nd:YAG laser and SRP; while the "control side " was treated with SRP alone. At baseline, and after a median follow-up time of 20 months (range 12-39), periodontal inflammatory parameters (plaque index [PI], gingival index [GI], probing pocket depth [PPD]), and marginal bone loss (on digital bite-wing radiographs) were measured. Gingival crevicular fluid (GCF) was collected from the teeth 35, 36, 45, and 46 at baseline and at follow-up. Pl (p < 0.01), GI (p < 0.01), and PPD (p < 0.001) were significantly lower on the test side compared to the control side at follow-up. Radiological results showed significantly less bone loss on the test side compared to the control side (p < 0.05). GCF volume was lower on the test side compared to the control side (p < 0.01). In conclusion, a single application of Nd:YAG laser in combination with SRP had a positive long-term effect on periodontal health compared to treatment by SRP alone.