Purpose: The purpose of this randomized single-blind controlled trial was to elucidate the clinical and antimicrobial effects of daily phototherapy (PT) as an adjunct to scaling and root planing (SRP) in patients with chronic periodontitis. Methods: The study was conducted from December 2013 to May 2014 at Ewha Womans University Mokdong Hospital, Seoul, Korea. Forty-one patients with mild to moderate chronic periodontitis were randomly divided into two therapeutic groups in a 1:1 ratio: SRP+PT and SRP (control) groups. All participants underwent full-mouth SRP. PT was performed thrice a day for a month by using electric toothbrushes with embedded light-emitting diodes. Plaque index, gingival index, probing pocket depth (PPD), clinical attachment level (CAL), and bleeding on probing were assessed before (baseline) and four weeks after (follow-up) the treatment. Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Prevotella intermedia, Fusobacterium nucleatum, Parvimonas micra, Campylobacter rectus, Eikenella corrodens, Streptococcus mutans, and Streptococcus sobrinus levels were detected by a real-time polymerase chain reaction at the same points in time. Results: The clinical parameters improved in both the groups. At the follow-up assessment, PPD was significantly decreased in the SRP+PT group (P=0.00). Further, PPD and CAL showed significantly greater changes in the SRP+PT group than in the SRP group (PPD, P=0.03; CAL, P=0.04). P. gingivalis and T. forsythia levels decreased in this group, but no significant intergroup differences were noted. Conclusions: Adjunctive PT seems to have clinical benefits, but evidence of its antimicrobial effects is not sufficient. Long-term studies are necessary to develop the most effective PT protocol and compare the effectiveness of PT with and without exogenous photosensitizers.