Objective: The purpose of this study was to evaluate the clinical use of an erbium, chromium: yttrium–scandium–gallium–garnet (Er,Cr:YSGG) laser in the management of root furcation involvements. Background data: It has been suggested that the use of laser radiation within the periodontal pocket may be effective in periodontal treatment. However, very limited data from clinical trials exist directly comparing the use of the Er,Cr:YSGG laser to conventional root planing. Materials and methods: Thirty patients with chronic periodontitis were recruited. A total of 128 teeth with degree II or III furcation involvement were included in a split-mouth design such that the teeth on one side of the mouth were established as Group A and treated with the Er,Cr:YSGG laser and the teeth on the other side were established as Group B and treated with manual subgingival debridement. Changes in probing depth (PD), bleeding on probing (BOP), clinical attachment loss (CAL), and visual analogue scale (VAS) pain scores were compared between Groups A and B and within individuals over time at 6 and 12 weeks after treatment, testing the null hypothesis that there would be no clinical difference between treatment modalities. Results: Both treatments significantly reduced the PD, CAL, and BOP in the diseased teeth with degree II or III furcation involvement. The reduction of PD and BOP at weeks 6 and 12 was significantly higher in Group A (laser treated) than in Group B. The VAS pain score was significantly lower in Group A than in Group B ( p < 0.01). Conclusions: Pocket debridement with Er,Cr:YSGG laser is a safe, comfortable, and clinically effective means of subgingival debridement in periodontal therapy.