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The erbium-doped yttrium, aluminum, and garnet (Er:YAG) laser is thought to be the most promising laser for periodontal treatment; however, its application is still under consideration. The aim of this study was to compare Er:YAG laser monotherapy with conventional scaling and root planing (SRP) for chronic periodontitis using clinical parameters, the detection rate of periodontal pathogens, and the calprotectin level in gingival crevicular fluid.Twenty-seven participants with moderate-to-advanced chronic periodontitis were included. In a split-mouth design, the 2 half-mouths of each participant were randomly assigned to Er:YAG laser or SRP (combination of ultrasonic and manual instruments) treatment. Clinical parameters were recorded at baseline, 6 weeks, and 3 and 6 months after treatment. At the same time points, gingival crevicular fluid was collected to analyze the detection rate of 6 periodontal pathogens by polymerase chain reaction and the levels of calprotectin by enzyme-linked immunosorbent assay.Both treatment groups showed significant reductions in probing depth (PD), bleeding index (BI), and clinical attachment level (CAL) from baseline to 6 months. For sites with 4 mm ≤ PD ≤ 6 mm at baseline, SRP resulted in a greater reduction in PD and CAL than Er:YAG laser treatment, and the difference remained at 6 months post-treatment (P = .01 and P < .01, respectively). For sites with PD ≥7 mm at baseline, the clinical parameters showed similar results between the 2 groups. SRP resulted in a lower detection rate of Porphyromonas gingivalis at 6 months post-treatment. The levels of calprotectin were significantly decreased from baseline to 6 months in both groups, without a significant difference between the groups.For mild pockets, conventional SRP may still be the preferred choice. For deep pockets, Er:YAG laser treatment could be an effective alternative. Studies are needed to explore more advanced instruments and new application methods for the Er:YAG laser for periodontal treatment in deep pockets.