Purpose: Tetracycline and its chemically modified non-antibacterial analogues can inhibit certain host-derived tissue destructive collagenases such as matrix metalloproteinases. The purpose of this study was to evaluate clinical and microbiologic effects of the subantimicrobial dose of doxycycline(SDD) in conjunction with scaling and root planing. Materials and methods: A total of 30 patients with chronic periodontitis who were going to receive scaling and root planing were randomly allocated to receive either a doxycycline hyclate for 3 months or nothing. Clinical probing depth, clinical attachment level, gingival recession, and bleeding on probing were measured by one periodontist. After a periodontal examination, microbial samples were collected using sterile paper points. The effect of SDD in conjunction with scaling and root planing on alterations of the periodontal pathogens (Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Porphyromonas gingivalis) were also assessed using l6S rRNA polymerase chain reaction. Results: During the treatment period, clinical parameters for both treatment group and control group were improved. After 3 months, reductions in probing depth and gains in clinical attachment level were significantly greater for the SDD group than control group. Microbial analysis showed that there was no alteration of the periodontal pathogens and no difference between the groups. Conclusion: This study suggested that the subantimicrobial dose of doxycycline as an adjunct therapy with scaling and root planing might be effective and safe in the management of chronic periodontitis.